add source for exercise 11
This commit is contained in:
Andrew Straw
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57c6d310c3
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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-6eb17f6ff50e7d3d",
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"locked": true,
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"schema_version": 3,
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"solution": false,
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"task": false
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},
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"tags": []
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},
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"source": [
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"# Bioinformatics introduction"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-946d22188d87a0a5",
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"locked": true,
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"schema_version": 3,
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"solution": false,
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"task": false
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},
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"tags": []
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},
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"source": [
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"In this exercise, you will perform some bioinformatic analysis. There is no specific correct answer here, but rather a series of tasks which to fulfill. You are encouraged to use online resources and discussions with colleagues to help you at all stages.\n",
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"\n",
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"The majority of the work for this exercise is manually interacting with websites and understanding what types of data they use and first steps of using the online tools. The Python here is mainly used as a path for you to follow through the steps one-by-one.\n",
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"\n",
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"Pick a protein-coding gene interesting to you. In case you cannot think of anything, I suggest: ACE2, TP53, TGFbeta1, Drosophila DopEcR, TAS1R2, Drosophila nAChRalpha1. Find the gene at [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene).\n",
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"\n",
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"## Task 1: What is the full name of this gene? What is the NCBI GeneID?"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"nbgrader": {
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"grade": true,
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"grade_id": "cell-f26307b555211aca",
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"locked": false,
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"points": 1,
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"schema_version": 3,
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"solution": true,
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"task": false
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}
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},
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"source": [
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"Drosophila nAChRalpha1, GeneID:42918"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-b9777b8be7bc0ad5",
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"locked": true,
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"schema_version": 3,
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"solution": false,
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"task": false
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},
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"tags": []
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},
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"source": [
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"Find the complete sequence for one protein isoform using [NCBI protein database website](https://www.ncbi.nlm.nih.gov/protein/). Hint: it may be easier to find the protein sequence after first finding the gene at [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene), go to \"RefSeq\" sequences and then clicking on the protein sequence, which will probably start with `NP_`.\n",
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"\n",
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"Download a FASTA file with the seqence of this protein isoform.\n",
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"\n",
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"## Task 2: Make a variable named `original_fasta` which is a string containing the FASTA format protein sequence\n",
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"\n",
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"You can create a multi-line string in Python with triple quotes like this:\n",
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"\n",
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"```python\n",
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"my_string = \"\"\"line 1\n",
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"line 2\n",
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"line 3\"\"\"\n",
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"```\n",
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"\n",
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"Or this this:\n",
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"\n",
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"```python\n",
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"my_string = '''line 1\n",
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"line 2\n",
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"line 3'''\n",
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"```"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-c81dad73272cc1d7",
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"locked": false,
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"schema_version": 3,
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"solution": true,
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"task": false
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}
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},
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"outputs": [],
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"source": [
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"original_fasta = \"\"\">NP_001262917.1 nicotinic acetylcholine receptor alpha1, isoform C [Drosophila melanogaster]\n",
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"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAADLSPTFEKPYAREMEKTIEGSRFIAQH\n",
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"VKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKFELLK\n",
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"MGSENTL\"\"\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Requirement already satisfied: biopython in /Users/andrew/anaconda3/envs/wm01-dragon/lib/python3.11/site-packages (1.84)\n",
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"Requirement already satisfied: numpy in /Users/andrew/anaconda3/envs/wm01-dragon/lib/python3.11/site-packages (from biopython) (1.26.4)\n"
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]
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}
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],
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"source": [
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"# Ensure that we have the biopython package installed\n",
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"!pip install biopython"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {
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"nbgrader": {
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"grade": true,
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"grade_id": "cell-7a1036cfda280feb",
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"locked": true,
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"points": 1,
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"schema_version": 3,
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"solution": false,
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"task": false
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}
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},
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"outputs": [],
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"source": [
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"# This is a test of the above, do not change this code.\n",
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"import io\n",
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"import Bio.SeqIO\n",
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"records = [record for record in Bio.SeqIO.parse(io.StringIO(original_fasta), \"fasta\")]\n",
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"assert len(records)==1\n",
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"assert isinstance(records[0], Bio.SeqRecord.SeqRecord)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-96024e67e7e5036e",
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"locked": true,
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"schema_version": 3,
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"solution": false,
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"task": false
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},
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"tags": []
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},
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"source": [
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"Now perform a protein BLAST search for homologous sequences using [the NCBI BLAST website](https://blast.ncbi.nlm.nih.gov/Blast.cgi).\n",
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"\n",
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"View the FASTA data with these sequences for at least 5 total sequences. Do not take other isoforms of the same gene in the same species. Take either: A) other genes in the same species or B) potentially homologous genes in other species. Do not take both A and B. You may limit your search to specific species to fulfill these criteria or your own curiosity.\n",
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"\n",
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"## Task 3: Make a variable named `others` which is a list of strings containing the FASTA format protein sequences"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-f4f84628865fc2ec",
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"locked": false,
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"schema_version": 3,
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"solution": true,
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"task": false
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}
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},
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"outputs": [],
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"source": [
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"# Type your answer here and then run this and the following cell.\n",
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"others = [\n",
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" \"\"\">XP_001981981.3 acetylcholine receptor subunit alpha-like 1 [Drosophila erecta]\n",
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"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAAAAAADLSPTFEKPYAREMEKTIEG\n",
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"SRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAK\n",
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"KKFELLKMGSENTL\"\"\",\n",
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" \"\"\">XP_017020195.1 PREDICTED: acetylcholine receptor subunit alpha-like 1 isoform X1 [Drosophila kikkawai]\n",
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"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FGEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRFI\n",
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"AQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKFE\n",
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"LLKMGSENTL\"\"\",\n",
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" \"\"\">XP_037710630.1 acetylcholine receptor subunit alpha-like 1 [Drosophila subpulchrella]\n",
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"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRFI\n",
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"AQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKFE\n",
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"LLKMGSDNTL\"\"\",\n",
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" \"\"\">XP_002032513.1 acetylcholine receptor subunit alpha-like 1 [Drosophila sechellia]\n",
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"MGSVLFTAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRF\n",
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"IAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKF\n",
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"ELLKMGSENTL\"\"\",\n",
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" \"\"\">XP_017009134.1 PREDICTED: acetylcholine receptor subunit alpha-like 1 [Drosophila takahashii]\n",
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"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRF\n",
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"IAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKF\n",
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"ELLKMGSDNTL\"\"\"\n",
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"]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {
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"nbgrader": {
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"grade": true,
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"grade_id": "cell-0ef639671dbc2b53",
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"locked": true,
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"points": 1,
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"schema_version": 3,
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"solution": false,
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"task": false
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}
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},
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"outputs": [],
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"source": [
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"# This is a test of the above, do not change this code.\n",
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"assert len(others)>=5\n",
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"seen = [original_fasta]\n",
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"for this_fasta in others:\n",
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" assert type(this_fasta)==str\n",
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" assert this_fasta not in seen \n",
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" records = [record for record in Bio.SeqIO.parse(io.StringIO(this_fasta), \"fasta\")]\n",
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" assert len(records)==1"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-e62c5138daab0413",
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"locked": true,
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"schema_version": 3,
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"solution": false,
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"task": false
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},
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"tags": []
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},
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"source": [
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"Now, let's join your original fasta data and the data you found with BLAST all together in one big multi-sequence FASTA data string.\n",
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"\n",
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"FASTA files can have multiple sequences in one file just by *concatenating* (or \"joining\" or \"adding\") them together."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {
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"nbgrader": {
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"grade": false,
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"grade_id": "cell-bbfd775731cacd7d",
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"locked": true,
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"schema_version": 3,
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"solution": false,
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"task": false
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},
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"tags": []
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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">NP_001262917.1 nicotinic acetylcholine receptor alpha1, isoform C [Drosophila melanogaster]\n",
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"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAADLSPTFEKPYAREMEKTIEGSRFIAQH\n",
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"VKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKFELLK\n",
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"MGSENTL\n",
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">XP_001981981.3 acetylcholine receptor subunit alpha-like 1 [Drosophila erecta]\n",
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"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
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"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
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"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
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"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
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"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
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"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
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"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAAAAAADLSPTFEKPYAREMEKTIEG\n",
|
||||
"SRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAK\n",
|
||||
"KKFELLKMGSENTL\n",
|
||||
">XP_017020195.1 PREDICTED: acetylcholine receptor subunit alpha-like 1 isoform X1 [Drosophila kikkawai]\n",
|
||||
"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
|
||||
"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
|
||||
"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
|
||||
"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
|
||||
"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
|
||||
"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
|
||||
"FGEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRFI\n",
|
||||
"AQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKFE\n",
|
||||
"LLKMGSENTL\n",
|
||||
">XP_037710630.1 acetylcholine receptor subunit alpha-like 1 [Drosophila subpulchrella]\n",
|
||||
"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
|
||||
"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
|
||||
"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
|
||||
"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
|
||||
"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
|
||||
"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
|
||||
"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRFI\n",
|
||||
"AQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKFE\n",
|
||||
"LLKMGSDNTL\n",
|
||||
">XP_002032513.1 acetylcholine receptor subunit alpha-like 1 [Drosophila sechellia]\n",
|
||||
"MGSVLFTAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
|
||||
"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
|
||||
"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
|
||||
"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
|
||||
"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
|
||||
"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
|
||||
"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRF\n",
|
||||
"IAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKF\n",
|
||||
"ELLKMGSENTL\n",
|
||||
">XP_017009134.1 PREDICTED: acetylcholine receptor subunit alpha-like 1 [Drosophila takahashii]\n",
|
||||
"MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\n",
|
||||
"MTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\n",
|
||||
"PPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\n",
|
||||
"VPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\n",
|
||||
"SLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\n",
|
||||
"KLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\n",
|
||||
"FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAAADLSPTFEKPYAREMEKTIEGSRF\n",
|
||||
"IAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKF\n",
|
||||
"ELLKMGSDNTL\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"all_list = [original_fasta] + others\n",
|
||||
"all_string = '\\n'.join(all_list)\n",
|
||||
"print(all_string)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-5d4a627513248352",
|
||||
"locked": true,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
},
|
||||
"tags": []
|
||||
},
|
||||
"source": [
|
||||
"## Task 4: Perform multi-species alignment using [Clustal Omega at the EBI website](https://www.ebi.ac.uk/jdispatcher/msa/clustalo).\n",
|
||||
"\n",
|
||||
"This website runs multiple sequence alignment software. You can directly upload the multiple sequence FASTA file you generated above and let their computer do the alignment.\n",
|
||||
"\n",
|
||||
"Cut and paste the multiple sequence FASTA above into the Clustal Omega entry page at the EBI website. Keep all parameters at their default values (Protein, Output format ClustalW with character counts).\n",
|
||||
"\n",
|
||||
"Enter the multi-sequence alignment here below as a multi-line string called `msa`."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 8,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-6ffef2e19f573e15",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This is a test of the above, do not change this code.\n",
|
||||
"msa = \"\"\"CLUSTAL O(1.2.4) multiple sequence alignment\n",
|
||||
"\n",
|
||||
"\n",
|
||||
"XP_017020195.1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQ\t60\n",
|
||||
"XP_037710630.1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQ\t60\n",
|
||||
"XP_002032513.1 MGSVLFTAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQ\t60\n",
|
||||
"XP_017009134.1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQ\t60\n",
|
||||
"NP_001262917.1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQ\t60\n",
|
||||
"XP_001981981.3 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQ\t60\n",
|
||||
" ******:*****************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 LIDVNLKNQIMTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGN\t120\n",
|
||||
"XP_037710630.1 LIDVNLKNQIMTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGN\t120\n",
|
||||
"XP_002032513.1 LIDVNLKNQIMTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGN\t120\n",
|
||||
"XP_017009134.1 LIDVNLKNQIMTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGN\t120\n",
|
||||
"NP_001262917.1 LIDVNLKNQIMTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGN\t120\n",
|
||||
"XP_001981981.3 LIDVNLKNQIMTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGN\t120\n",
|
||||
" ************************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 YEVTIMTKAILHHTGKVVWKPPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLR\t180\n",
|
||||
"XP_037710630.1 YEVTIMTKAILHHTGKVVWKPPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLR\t180\n",
|
||||
"XP_002032513.1 YEVTIMTKAILHHTGKVVWKPPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLR\t180\n",
|
||||
"XP_017009134.1 YEVTIMTKAILHHTGKVVWKPPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLR\t180\n",
|
||||
"NP_001262917.1 YEVTIMTKAILHHTGKVVWKPPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLR\t180\n",
|
||||
"XP_001981981.3 YEVTIMTKAILHHTGKVVWKPPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLR\t180\n",
|
||||
" ************************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 HLKQTADSDNIEVGIDLQDYYISVEWDIMRVPAVRNEKFYSCCEEPYLDIVFNLTLRRKT\t240\n",
|
||||
"XP_037710630.1 HLKQTADSDNIEVGIDLQDYYISVEWDIMRVPAVRNEKFYSCCEEPYLDIVFNLTLRRKT\t240\n",
|
||||
"XP_002032513.1 HLKQTADSDNIEVGIDLQDYYISVEWDIMRVPAVRNEKFYSCCEEPYLDIVFNLTLRRKT\t240\n",
|
||||
"XP_017009134.1 HLKQTADSDNIEVGIDLQDYYISVEWDIMRVPAVRNEKFYSCCEEPYLDIVFNLTLRRKT\t240\n",
|
||||
"NP_001262917.1 HLKQTADSDNIEVGIDLQDYYISVEWDIMRVPAVRNEKFYSCCEEPYLDIVFNLTLRRKT\t240\n",
|
||||
"XP_001981981.3 HLKQTADSDNIEVGIDLQDYYISVEWDIMRVPAVRNEKFYSCCEEPYLDIVFNLTLRRKT\t240\n",
|
||||
" ************************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 LFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILLSLTVFFLLLAEIIPPTSLTV\t300\n",
|
||||
"XP_037710630.1 LFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILLSLTVFFLLLAEIIPPTSLTV\t300\n",
|
||||
"XP_002032513.1 LFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILLSLTVFFLLLAEIIPPTSLTV\t300\n",
|
||||
"XP_017009134.1 LFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILLSLTVFFLLLAEIIPPTSLTV\t300\n",
|
||||
"NP_001262917.1 LFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILLSLTVFFLLLAEIIPPTSLTV\t300\n",
|
||||
"XP_001981981.3 LFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILLSLTVFFLLLAEIIPPTSLTV\t300\n",
|
||||
" ************************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 PLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILPKLLCIERPKK\t360\n",
|
||||
"XP_037710630.1 PLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILPKLLCIERPKK\t360\n",
|
||||
"XP_002032513.1 PLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILPKLLCIERPKK\t360\n",
|
||||
"XP_017009134.1 PLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILPKLLCIERPKK\t360\n",
|
||||
"NP_001262917.1 PLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILPKLLCIERPKK\t360\n",
|
||||
"XP_001981981.3 PLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILPKLLCIERPKK\t360\n",
|
||||
" ************************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 EEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\t420\n",
|
||||
"XP_037710630.1 EEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\t420\n",
|
||||
"XP_002032513.1 EEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\t420\n",
|
||||
"XP_017009134.1 EEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\t420\n",
|
||||
"NP_001262917.1 EEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\t420\n",
|
||||
"XP_001981981.3 EEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\t420\n",
|
||||
" ************************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 FGEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAA----AAAAADLSPTFEKPY\t476\n",
|
||||
"XP_037710630.1 FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAA----AAAAADLSPTFEKPY\t476\n",
|
||||
"XP_002032513.1 FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAA---AAAAADLSPTFEKPY\t477\n",
|
||||
"XP_017009134.1 FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAA---AAAAADLSPTFEKPY\t477\n",
|
||||
"NP_001262917.1 FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAA-------AAAADLSPTFEKPY\t473\n",
|
||||
"XP_001981981.3 FAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAAAAAAAAADLSPTFEKPY\t480\n",
|
||||
" *.************************************* **************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 AREMEKTIEGSRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQ\t536\n",
|
||||
"XP_037710630.1 AREMEKTIEGSRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQ\t536\n",
|
||||
"XP_002032513.1 AREMEKTIEGSRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQ\t537\n",
|
||||
"XP_017009134.1 AREMEKTIEGSRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQ\t537\n",
|
||||
"NP_001262917.1 AREMEKTIEGSRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQ\t533\n",
|
||||
"XP_001981981.3 AREMEKTIEGSRFIAQHVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQ\t540\n",
|
||||
" ************************************************************\n",
|
||||
"\n",
|
||||
"XP_017020195.1 APSLYDQSQPIDILYSKIAKKKFELLKMGSENTL\t570\n",
|
||||
"XP_037710630.1 APSLYDQSQPIDILYSKIAKKKFELLKMGSDNTL\t570\n",
|
||||
"XP_002032513.1 APSLYDQSQPIDILYSKIAKKKFELLKMGSENTL\t571\n",
|
||||
"XP_017009134.1 APSLYDQSQPIDILYSKIAKKKFELLKMGSDNTL\t571\n",
|
||||
"NP_001262917.1 APSLYDQSQPIDILYSKIAKKKFELLKMGSENTL\t567\n",
|
||||
"XP_001981981.3 APSLYDQSQPIDILYSKIAKKKFELLKMGSENTL\t574\n",
|
||||
" ******************************:***\n",
|
||||
"\"\"\""
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 9,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-b39fdf740eda5d89",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This is a test of the above, do not change this code.\n",
|
||||
"records = [record for record in Bio.SeqIO.parse(io.StringIO(msa), \"clustal\")]\n",
|
||||
"assert len(records)>=6"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"celltoolbar": "Create Assignment",
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3 (ipykernel)",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.11.7"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 4
|
||||
}
|
||||
472
exercises/source/exercise-11/2__making_HTTP_get_calls.ipynb
Normal file
472
exercises/source/exercise-11/2__making_HTTP_get_calls.ipynb
Normal file
|
|
@ -0,0 +1,472 @@
|
|||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 1,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Import libraries we need\n",
|
||||
"import requests\n",
|
||||
"import urllib.parse"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 2,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# You must run this cell, but you can ignore its contents.\n",
|
||||
"import hashlib\n",
|
||||
"\n",
|
||||
"def ads_hash(ty):\n",
|
||||
" \"\"\"Return a unique string for input\"\"\"\n",
|
||||
" ty_str = str(ty).encode()\n",
|
||||
" m = hashlib.sha256()\n",
|
||||
" m.update(ty_str)\n",
|
||||
" return m.hexdigest()[:10]"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 7,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"SWAPI_BASE='https://swapi.py4e.com/api/'\n",
|
||||
"\n",
|
||||
"def starwars_url(path):\n",
|
||||
" '''return a URL to the Star Wars API using SWAPI_BASE\n",
|
||||
" \n",
|
||||
" For example, to get the URL for person with ID 10,\n",
|
||||
" call:\n",
|
||||
" \n",
|
||||
" starwars_url('people/10/')\n",
|
||||
" '''\n",
|
||||
" return urllib.parse.urljoin(SWAPI_BASE,path)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"We need to be able to create an HTTP request to get a particular person from SWAPI. We are going to be making HTTP GET requests using the URL to request the information we want. So, we need to create a String with the appropriate request. \n",
|
||||
"\n",
|
||||
"### Q1 Define a function which will take an integer as an argument and return a string, which is the URL to get that particular person from the SWAPI. Call your function `get_person_url`.\n",
|
||||
"\n",
|
||||
"For example for person 42, this function should return something like: `\"https://swapi.dev/api/people/42/\"`. However, the URL should be made with the `starwars_url()` function so that it starts with the value `SWAPI_BASE` (and not necessarily `https://swapi.dev/api`). This is useful in case the website changes location or in case we decide to start hosting our own copy of the website at a different URL."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 8,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-496b12c0d3e2489f",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Write your answer here\n",
|
||||
"def get_person_url(person_id):\n",
|
||||
" url = starwars_url('people/%d/'%person_id)\n",
|
||||
" return url"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 9,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-b3a7ebab227918e4",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This checks that the above worked\n",
|
||||
"person_10_url = get_person_url(10)\n",
|
||||
"assert(type(person_10_url)==str)\n",
|
||||
"assert(person_10_url.startswith(SWAPI_BASE))\n",
|
||||
"assert(person_10_url.endswith('people/10') or person_10_url.endswith('people/10/'))"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"Now, let's use the Python `requests` library to make an HTTP GET call to this URL. View its documentation at https://docs.python-requests.org/en/latest/.\n",
|
||||
"\n",
|
||||
"### Q2 Using your `get_person_url()` function, create a variable called `person_url` for person 10. Now, assign the result of `requests.get(person_url)` to a variable called `response`."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 10,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-65e02d72fd413542",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Write your answer here\n",
|
||||
"person_url = get_person_url(10)\n",
|
||||
"response = requests.get(person_url)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 11,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-cbc105eff3987aa9",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This checks that the above worked\n",
|
||||
"assert ads_hash(response.json()['name'])=='6e84377ee7'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"Now let's wrap this up in a function which takes a person ID number and returns a dictionary for that person using the `response.json()` method from `requests`.\n",
|
||||
"\n",
|
||||
"### Q3 Make a function called `get_person` which takes an integer as an argument and returns a dict with the result from the SWAPI"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 12,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-11010cba389895bd",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Write your answer here\n",
|
||||
"def get_person(person_id):\n",
|
||||
" url = get_person_url(person_id)\n",
|
||||
" response = requests.get(url)\n",
|
||||
" return response.json()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 13,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-9c11e54ba69189a0",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This checks that the above worked\n",
|
||||
"assert ads_hash(get_person(1)['name'])=='9d00804504'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## HTTP POST requests\n",
|
||||
"\n",
|
||||
"Up to now, we have been using HTTP GET requests. These are what your browser does when you go to a webpage and are good for getting information.\n",
|
||||
"\n",
|
||||
"Sometimes, however, we want to upload more complicated data to another program. This is often done with the HTTP POST request.\n",
|
||||
"\n",
|
||||
"Here we are going to POST data to a server which will add a value to our input."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 14,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"ADDER_URL = 'http://http-demo-server.strawlab.org/'\n",
|
||||
"response = requests.post(ADDER_URL+'add_to_value', json={'value':100})"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 15,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"200"
|
||||
]
|
||||
},
|
||||
"execution_count": 15,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"# Any status code other than 200 is an error\n",
|
||||
"response.status_code"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 16,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"'{\"value\":142}'"
|
||||
]
|
||||
},
|
||||
"execution_count": 16,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"response.text"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 17,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"{'value': 142}"
|
||||
]
|
||||
},
|
||||
"execution_count": 17,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"response.json()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Q4 What is the value added the the input by the HTTP server? Put your answer in the variable `added`."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 18,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-6f8a3c2b5f23135e",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Write your answer here\n",
|
||||
"added = 42"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 19,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-60ba73a7486b8988",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This checks that the above worked\n",
|
||||
"assert ads_hash(added)=='73475cb40a'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Q5 There is another path on our server called `mystery`. It works similarly to `add_to_value`. What is the JSON `value` returned by this HTTP endpoint when called with an input value of 100? Put your answer in the variable `mystery100`."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 20,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-51d14040f23943ad",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Write your answer here\n",
|
||||
"mystery100 = requests.post(ADDER_URL+'mystery', json={'value':100}).json()['value']"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 21,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-3392fa03f78e9c65",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This checks that the above worked\n",
|
||||
"assert ads_hash(mystery100)=='26d228663f'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Q6 Play around with this `mystery` until you think you understand what it is doing. Now make a function called `myfunc` which takes a single integer argument and returns an integer which should do the same thing as the mystery HTTP endpoint."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 22,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-cc8f1c957dc44cd2",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Write your answer here\n",
|
||||
"def myfunc(value):\n",
|
||||
" return value*4"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 23,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-b48cf735571f569b",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This checks that the above worked\n",
|
||||
"assert ads_hash(type(myfunc))=='ac75372cfc' \n",
|
||||
"assert ads_hash(myfunc(3))=='6b51d431df'\n",
|
||||
"assert ads_hash(myfunc(5))=='f5ca38f748'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"# What have we learned here?\n",
|
||||
"\n",
|
||||
"HTTP is the \"language\" (protocol, to be technically correct) that your web browser uses to get webpages and images on the internet. More than that, it is also a useful language for computer programs to talk to each other on the internet.\n",
|
||||
"\n",
|
||||
"(HTTPS is just a secure version of HTTP. This means it is encrypted and there is a cryptographic \"chain of trust\" to the owner of the domain name.)\n",
|
||||
"\n",
|
||||
"GET requests typically just get a certain resource.\n",
|
||||
"\n",
|
||||
"POST requests often send more data to the server. The server then does something with this data.\n",
|
||||
"\n",
|
||||
"There are other HTTP request types, but GET and POST are the dominant ones.\n",
|
||||
"\n",
|
||||
"There are zillions of data sources on the internet that you can access with HTTP."
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"celltoolbar": "Create Assignment",
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3 (ipykernel)",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.11.7"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 4
|
||||
}
|
||||
984
exercises/source/exercise-11/3__bioinformatics_with_HTTP.ipynb
Normal file
984
exercises/source/exercise-11/3__bioinformatics_with_HTTP.ipynb
Normal file
|
|
@ -0,0 +1,984 @@
|
|||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 1,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Import biopython\n",
|
||||
"import Bio\n",
|
||||
"\n",
|
||||
"import requests"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 2,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# You must run this cell, but you can ignore its contents.\n",
|
||||
"\n",
|
||||
"import hashlib\n",
|
||||
"\n",
|
||||
"def ads_hash(ty):\n",
|
||||
" \"\"\"Return a unique string for input\"\"\"\n",
|
||||
" ty_str = str(ty).encode()\n",
|
||||
" m = hashlib.sha256()\n",
|
||||
" m.update(ty_str)\n",
|
||||
" return m.hexdigest()[:10]"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"# Bioinformatics with HTTP\n",
|
||||
"\n",
|
||||
"Not only can we use the Star Wars API with HTTP, we can also access the NCBI's databases over HTTP. Here is [more information from the NCBI](https://www.ncbi.nlm.nih.gov/books/NBK25499/). Note that in this exercise, we will be doing low volume queries without using a specialized software library. Some libraries and other software is available to automatically do this for here. For example, below we use the `NCBIWWW` module from biopython. Here we do it \"the hard way\" at a low level.\n",
|
||||
"\n",
|
||||
"If you start using the NCBI web resources extensively, please read the NCBI's documentation about [providing them with an email address to contact you](https://www.ncbi.nlm.nih.gov/books/NBK25497/).\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 3,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"def get_protein_fasta(accession):\n",
|
||||
" url = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=%s&rettype=fasta&retmode=text\"%(accession,)\n",
|
||||
" return requests.get(url).text"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 4,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"'>NP_524481.2 nicotinic acetylcholine receptor alpha1, isoform A [Drosophila melanogaster]\\nMGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQI\\nMTTNVWVEQEWNDYKLKWNPDDYGGVDTLHVPSEHIWLPDIVLYNNADGNYEVTIMTKAILHHTGKVVWK\\nPPAIYKSFCEIDVEYFPFDEQTCFMKFGSWTYDGYMVDLRHLKQTADSDNIEVGIDLQDYYISVEWDIMR\\nVPAVRNEKFYSCCEEPYLDIVFNLTLRRKTLFYTVNLIIPCVGISFLSVLVFYLPSDSGEKISLCISILL\\nSLTVFFLLLAEIIPPTSLTVPLLGKYLLFTMMLVTLSVVVTIAVLNVNFRSPVTHRMAPWVQRLFIQILP\\nKLLCIERPKKEEPEEDQPPEVLTDVYHLPPDVDKFVNYDSKRFSGDYGIPALPASHRFDLAAAGGISAHC\\nFAEPPLPSSLPLPGADDDLFSPSGLNGDISPGCCPAAAAAAAADLSPTFEKPYAREMEKTIEGSRFIAQH\\nVKNKDKFESVEEDWKYVAMVLDRMFLWIFAIACVVGTALIILQAPSLYDQSQPIDILYSKIAKKKFELLK\\nMGSENTL\\n\\n'"
|
||||
]
|
||||
},
|
||||
"execution_count": 4,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"da1 = get_protein_fasta('NP_524481.2')\n",
|
||||
"da1"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"Great, so we can get FASTA files directly from the NBCI using the accession.\n",
|
||||
"\n",
|
||||
"### Q1 Get the FASTA for accession `NP_733001.1`. Put the result in the variable `da2`, which should be a string."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": false,
|
||||
"grade_id": "cell-570ab47725befb18",
|
||||
"locked": false,
|
||||
"schema_version": 3,
|
||||
"solution": true,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Write your answer here\n",
|
||||
"da2 = get_protein_fasta('NP_733001.1')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 6,
|
||||
"metadata": {
|
||||
"nbgrader": {
|
||||
"grade": true,
|
||||
"grade_id": "cell-5c1c1943259aebbb",
|
||||
"locked": true,
|
||||
"points": 1,
|
||||
"schema_version": 3,
|
||||
"solution": false,
|
||||
"task": false
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# This checks that the above worked\n",
|
||||
"assert ads_hash(da2)=='16538bd802'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"# Using the biopython library for bioinformatics, including NCBI queries"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 7,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import Bio\n",
|
||||
"from Bio.Blast import NCBIWWW\n",
|
||||
"from Bio.Blast import NCBIXML\n",
|
||||
"from Bio import SeqIO\n",
|
||||
"from io import StringIO\n",
|
||||
"import os"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"We can work with FASTA sequences using the biopython library. It expects multiple sequences in a given FASTA file, so we loop over them:\n",
|
||||
"\n",
|
||||
"Each record here is an instance of the [Seq class](https://biopython.org/wiki/Seq).\n",
|
||||
"\n",
|
||||
"Let's copy the sequence to a raw python string called `da2_seq`:"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 8,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"ID: NP_733001.1\n",
|
||||
"Name: NP_733001.1\n",
|
||||
"Description: NP_733001.1 nicotinic acetylcholine receptor alpha2, isoform B [Drosophila melanogaster]\n",
|
||||
"Number of features: 0\n",
|
||||
"Seq('MAPGCCTTRPRPIALLAHIWRHCKPLCLLLVLLLLCETVQANPDAKRLYDDLLS...KKN')\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"da2_seq = None\n",
|
||||
"for record in SeqIO.parse(StringIO(da2), \"fasta\"):\n",
|
||||
" print(record)\n",
|
||||
" assert(da2_seq is None)\n",
|
||||
" da2_seq = str(record.seq)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"'MAPGCCTTRPRPIALLAHIWRHCKPLCLLLVLLLLCETVQANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQILTTNVWLEHEWQDHKFKWDPSEYGGVTELYVPSEHIWLPDIVLYNNADGEYVVTTMTKAILHYTGKVVWTPPAIFKSSCEIDVRYFPFDQQTCFMKFGSWTYDGDQIDLKHISQKNDKDNKVEIGIDLREYYPSVEWDILGVPAERHEKYYPCCAEPYPDIFFNITLRRKTLFYTVNLIIPCVGISYLSVLVFYLPADSGEKIALCISILLSQTMFFLLISEIIPSTSLALPLLGKYLLFTMLLVGLSVVITIIILNIHYRKPSTHKMRPWIRSFFIKRLPKLLLMRVPKDLLRDLAANKINYGLKFSKTKFGQALMDEMQMNSGGSSPDSLRRMQGRVGAGGCNGMHVTTATNRFSGLVGALGGGLSTLSGYNGLPSVLSGLDDSLSDVAARKKYPFELEKAIHNVMFIQHHMQRQDEFNAEDQDWGFVAMVMDRLFLWLFMIASLVGTFVILGEAPSLYDDTKAIDVQLSDVAKQIYNLTEKKN'"
|
||||
]
|
||||
},
|
||||
"execution_count": 9,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"da2_seq"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"In addition to \"raw\" HTTP requests using the `requests` library, biopython also is able to call the NCBI for you. It is using HTTP to perform the call, but this is hidden from you. Below, we do a BLAST search based on the sequence we just downloaded."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"We can limit our search to just a few organisms using the NCBI taxon ID. The easiest way to find these it to start typing in the BLAST web search entry page and copy the taxon ID from there.\n",
|
||||
"\n",
|
||||
"Here are a few taxon IDs for some insects and then some code to limit our NCBI query just to these taxa."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"'txid30195[ORGN] OR txid7460[ORGN] OR txid7004[ORGN] OR txid7227[ORGN] OR txid7070[ORGN]'"
|
||||
]
|
||||
},
|
||||
"execution_count": 10,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"# Bombus terrestris 30195\n",
|
||||
"# Apis mellifera 7460\n",
|
||||
"# Locusta migratoria 7004\n",
|
||||
"# Drosophila melanogaster 7227\n",
|
||||
"# Tribolium castaneum 7070\n",
|
||||
"taxids = (30195, 7460, 7004, 7227, 7070)\n",
|
||||
"taxid_query = ' OR '.join(['txid%d[ORGN]'%taxid for taxid in taxids])\n",
|
||||
"taxid_query"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"Now with our query limited to these specific groups, we are going to run a BLAST search. As with the web browser interface, this can take some time, so the code below is written to only run the web search when the output file is not present. Therefore, once you run the web search the first time, it will not run again unless you delete the file.\n",
|
||||
"\n",
|
||||
"Futhermore, as [mentioned in the bio python tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc92), we need to be careful with our result handle when we get it because it can be read only once. So, here we the results of our search to a local file. Later, we can read this as often as we want.\n",
|
||||
"\n",
|
||||
"**This may take some time as we are running a full BLAST search on the NCBI servers.**"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 11,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"not overwriting file da2_blast.xml\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"fname = \"da2_blast.xml\"\n",
|
||||
"if not os.path.exists(fname):\n",
|
||||
" result_handle = NCBIWWW.qblast(\"blastp\", \"nr\", da2_seq, entrez_query=taxid_query)\n",
|
||||
" with open(fname, \"w\") as out_handle:\n",
|
||||
" out_handle.write(result_handle.read())\n",
|
||||
"else:\n",
|
||||
" print(\"not overwriting file %s\"%fname)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 12,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"ref|NP_524482.1| nicotinic acetylcholine receptor alpha2, isoform A [Drosophila melanogaster] >ref|NP_733001.1| nicotinic acetylcholine receptor alpha2, isoform B [Drosophila melanogaster] >ref|XP_002032516.1| acetylcholine receptor subunit alpha-like 2 [Drosophila sechellia] >ref|XP_002104730.1| acetylcholine receptor subunit alpha-like 2 [Drosophila simulans] >ref|XP_033165329.1| acetylcholine receptor subunit alpha-like 2 [Drosophila mauritiana] >sp|P17644.1| RecName: Full=Acetylcholine receptor subunit alpha-like 2; AltName: Full=Nicotinic acetylcholine receptor alpha 2; Flags: Precursor [Drosophila melanogaster] >gb|ACL85307.1| nAcRalpha-96Ab-PA, partial [synthetic construct] >gb|AAF56302.2| nicotinic acetylcholine receptor alpha2, isoform A [Drosophila melanogaster] >gb|AAF56303.1| nicotinic acetylcholine receptor alpha2, isoform B [Drosophila melanogaster] >gb|AAL13675.1| GH22843p [Drosophila melanogaster] >gb|ACL90211.1| nAcRalpha-96Ab-PA [synthetic construct]\n",
|
||||
" Length = 576\n",
|
||||
"\n",
|
||||
"ref|NP_001011625.1| nicotinic acetylcholine receptor alpha2 subunit precursor [Apis mellifera] >ref|XP_006561565.1| nicotinic acetylcholine receptor alpha2 subunit isoform X1 [Apis mellifera] >ref|XP_026298380.1| nicotinic acetylcholine receptor alpha2 subunit isoform X1 [Apis mellifera] >gb|KAG6801311.1| nicotinic acetylcholine receptor alpha2 subunit precursor [Apis mellifera caucasica] >gb|KAG9431277.1| nicotinic acetylcholine receptor alpha2 subunit precursor [Apis mellifera carnica] >gb|AAS48080.1| neuronal nicotinic acetylcholine receptor Apisa2 subunit [Apis mellifera] >gb|AJE70260.1| nicotinic acetylcholine receptor alpha2 subunit [Apis mellifera]\n",
|
||||
" Length = 541\n",
|
||||
"\n",
|
||||
"ref|XP_003397559.1| acetylcholine receptor subunit alpha-L1 isoform X2 [Bombus terrestris]\n",
|
||||
" Length = 541\n",
|
||||
"\n",
|
||||
"ref|NP_001103423.1| nicotinic acetylcholine receptor alpha 2 subunit precursor [Tribolium castaneum] >gb|ABS86903.1| nicotinic acetylcholine receptor subunit alpha2 [Tribolium castaneum] >gb|EFA10793.1| nicotinic acetylcholine receptor subunit alpha2 [Tribolium castaneum]\n",
|
||||
" Length = 541\n",
|
||||
"\n",
|
||||
"ref|XP_012166790.1| acetylcholine receptor subunit alpha-L1 isoform X1 [Bombus terrestris]\n",
|
||||
" Length = 544\n",
|
||||
"\n",
|
||||
"gb|ACM09847.1| nicotinic acetylcholine receptor subunit a2 [Tribolium castaneum] >gb|ACM09848.1| nicotinic acetylcholine receptor subunit a2 [Tribolium castaneum] >gb|ACM09849.1| nicotinic acetylcholine receptor subunit a2 [Tribolium castaneum]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"gb|ACM09846.1| nicotinic acetylcholine receptor subunit a2 [Tribolium castaneum]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"gb|ACL00341.1| nicotinic acetylcholine receptor a2 subunit [Tribolium castaneum]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"ref|XP_008198426.1| PREDICTED: nicotinic acetylcholine receptor alpha 2 subunit isoform X1 [Tribolium castaneum]\n",
|
||||
" Length = 558\n",
|
||||
"\n",
|
||||
"gb|AHJ11209.1| nicotinic acetylcholine receptor alpha2 [Locusta migratoria]\n",
|
||||
" Length = 551\n",
|
||||
"\n",
|
||||
"ref|XP_015838943.1| PREDICTED: nicotinic acetylcholine receptor alpha 2 subunit isoform X2 [Tribolium castaneum]\n",
|
||||
" Length = 461\n",
|
||||
"\n",
|
||||
"ref|NP_001262917.1| nicotinic acetylcholine receptor alpha1, isoform C [Drosophila melanogaster] >ref|NP_524481.2| nicotinic acetylcholine receptor alpha1, isoform A [Drosophila melanogaster] >ref|XP_016952288.1| acetylcholine receptor subunit alpha-like 1 [Drosophila biarmipes] >sp|P09478.2| RecName: Full=Acetylcholine receptor subunit alpha-like 1; AltName: Full=Nicotinic acetylcholine receptor alpha 1; Flags: Precursor [Drosophila melanogaster] >gb|AAF56301.2| nicotinic acetylcholine receptor alpha1, isoform A [Drosophila melanogaster] >gb|AGB96297.1| nicotinic acetylcholine receptor alpha1, isoform C [Drosophila melanogaster]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"ref|NP_001262916.1| nicotinic acetylcholine receptor alpha1, isoform B [Drosophila melanogaster] >gb|AGB96296.1| nicotinic acetylcholine receptor alpha1, isoform B [Drosophila melanogaster]\n",
|
||||
" Length = 597\n",
|
||||
"\n",
|
||||
"ref|NP_001103245.1| nicotinic acetylcholine receptor alpha1 subunit precursor [Tribolium castaneum] >gb|ABS86902.1| nicotinic acetylcholine receptor subunit alpha1 [Tribolium castaneum] >gb|EEZ99265.1| nicotinic acetylcholine receptor subunit alpha1 [Tribolium castaneum]\n",
|
||||
" Length = 545\n",
|
||||
"\n",
|
||||
"emb|CAA30172.1| mature acetylcholine receptor alpha-like subunit [Drosophila melanogaster]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"gb|AHJ11220.1| nicotinic acetylcholine receptor alpha8 variant C [Locusta migratoria]\n",
|
||||
" Length = 574\n",
|
||||
"\n",
|
||||
"gb|AHJ11221.1| nicotinic acetylcholine receptor alpha8 variant D [Locusta migratoria]\n",
|
||||
" Length = 580\n",
|
||||
"\n",
|
||||
"gb|AHJ11218.1| nicotinic acetylcholine receptor alpha8 variant A [Locusta migratoria]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"gb|AHJ11219.1| nicotinic acetylcholine receptor alpha8 variant B [Locusta migratoria]\n",
|
||||
" Length = 546\n",
|
||||
"\n",
|
||||
"emb|CAA04053.1| nicotinic acetylcholine receptor, alpha2 subunit, partial [Locusta migratoria]\n",
|
||||
" Length = 515\n",
|
||||
"\n",
|
||||
"ref|NP_001091690.1| nicotinic acetylcholine receptor alpha1 subunit [Apis mellifera] >gb|AAY87890.1| nicotinic acetylcholine receptor alpha1 subunit [Apis mellifera] >gb|AJE70259.1| nicotinic acetylcholine receptor alpha1 subunit [Apis mellifera]\n",
|
||||
" Length = 601\n",
|
||||
"\n",
|
||||
"ref|XP_026298411.1| nicotinic acetylcholine receptor alpha1 subunit isoform X1 [Apis mellifera] >gb|KAG6801309.1| nicotinic acetylcholine receptor alpha1 subunit isoform X1 [Apis mellifera caucasica] >gb|KAG9431275.1| nicotinic acetylcholine receptor alpha1 subunit isoform X1 [Apis mellifera carnica]\n",
|
||||
" Length = 627\n",
|
||||
"\n",
|
||||
"ref|XP_003397561.2| acetylcholine receptor subunit alpha-like 1 [Bombus terrestris]\n",
|
||||
" Length = 615\n",
|
||||
"\n",
|
||||
"ref|XP_012163744.1| acetylcholine receptor subunit beta-like 2 isoform X1 [Bombus terrestris] >ref|XP_050590207.1| acetylcholine receptor subunit beta-like 2 isoform X1 [Bombus affinis]\n",
|
||||
" Length = 535\n",
|
||||
"\n",
|
||||
"ref|NP_001011575.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera] >gb|AAM51823.1| neuronal nicotinic acetylcholine receptor alpha-3 [Apis mellifera] >gb|AJE70266.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera]\n",
|
||||
" Length = 537\n",
|
||||
"\n",
|
||||
"ref|XP_012163745.1| acetylcholine receptor subunit beta-like 2 isoform X2 [Bombus terrestris] >ref|XP_050590208.1| acetylcholine receptor subunit beta-like 2 isoform X2 [Bombus affinis]\n",
|
||||
" Length = 531\n",
|
||||
"\n",
|
||||
"gb|KAG6799677.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera caucasica] >gb|KAG9434134.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera carnica]\n",
|
||||
" Length = 534\n",
|
||||
"\n",
|
||||
"ref|NP_001107770.1| nicotinic acetylcholine receptor alpha 3 subunit precursor [Tribolium castaneum] >ref|XP_008200302.1| PREDICTED: nicotinic acetylcholine receptor alpha 3 subunit isoform X1 [Tribolium castaneum] >gb|ABS86904.1| nicotinic acetylcholine receptor subunit alpha3 [Tribolium castaneum] >gb|ABV72695.1| nicotinic acetylcholine receptor alpha 3 subunit [Tribolium castaneum] >gb|ACM09844.1| nicotinic acetylcholine receptor subunit a3 [Tribolium castaneum] >gb|EEZ97689.1| nicotinic acetylcholine receptor subunit alpha3 [Tribolium castaneum]\n",
|
||||
" Length = 551\n",
|
||||
"\n",
|
||||
"ref|XP_026296304.1| nicotinic acetylcholine receptor alpha8 subunit isoform X1 [Apis mellifera]\n",
|
||||
" Length = 533\n",
|
||||
"\n",
|
||||
"ref|NP_001103419.1| nicotinic acetylcholine receptor alpha 8 subunit isoform 2 precursor [Tribolium castaneum] >gb|ABS86912.1| nicotinic acetylcholine receptor subunit alpha8 [Tribolium castaneum]\n",
|
||||
" Length = 508\n",
|
||||
"\n",
|
||||
"gb|ACP31314.1| nicotinic acetylcholine receptor a11 subunit [Tribolium castaneum]\n",
|
||||
" Length = 510\n",
|
||||
"\n",
|
||||
"ref|NP_001107771.1| nicotinic acetylcholine receptor alpha 11 subunit precursor [Tribolium castaneum] >gb|ABS86915.1| nicotinic acetylcholine receptor subunit alpha11 [Tribolium castaneum]\n",
|
||||
" Length = 510\n",
|
||||
"\n",
|
||||
"ref|NP_001155998.1| nicotinic acetylcholine receptor alpha 8 subunit isoform 1 precursor [Tribolium castaneum] >gb|ACP31302.1| nicotinic acetylcholine receptor a8 subunit splice variant [Tribolium castaneum] >gb|ACP31304.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum] >gb|ACP31305.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum] >gb|ACP31306.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum]\n",
|
||||
" Length = 515\n",
|
||||
"\n",
|
||||
"ref|XP_016767553.1| nicotinic acetylcholine receptor alpha3 subunit isoform X2 [Apis mellifera]\n",
|
||||
" Length = 553\n",
|
||||
"\n",
|
||||
"gb|KYB29425.1| nicotinic acetylcholine receptor subunit alpha11 [Tribolium castaneum]\n",
|
||||
" Length = 498\n",
|
||||
"\n",
|
||||
"gb|EEZ99341.2| nicotinic acetylcholine receptor subunit alpha8 [Tribolium castaneum]\n",
|
||||
" Length = 499\n",
|
||||
"\n",
|
||||
"gb|KYB29426.1| nicotinic acetylcholine receptor subunit alpha11 [Tribolium castaneum]\n",
|
||||
" Length = 491\n",
|
||||
"\n",
|
||||
"ref|XP_003399573.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus terrestris]\n",
|
||||
" Length = 554\n",
|
||||
"\n",
|
||||
"ref|NP_001073029.1| nicotinic acetylcholine receptor alpha3 subunit precursor [Apis mellifera] >ref|XP_016767550.1| nicotinic acetylcholine receptor alpha3 subunit isoform X1 [Apis mellifera] >ref|XP_016767551.1| nicotinic acetylcholine receptor alpha3 subunit isoform X1 [Apis mellifera] >ref|XP_016767552.1| nicotinic acetylcholine receptor alpha3 subunit isoform X1 [Apis mellifera] >gb|KAG6799381.1| nicotinic acetylcholine receptor alpha3 subunit precursor [Apis mellifera caucasica] >gb|KAG9433524.1| nicotinic acetylcholine receptor alpha3 subunit precursor [Apis mellifera carnica] >gb|AAY87891.1| nicotinic acetylcholine receptor alpha3 subunit [Apis mellifera]\n",
|
||||
" Length = 566\n",
|
||||
"\n",
|
||||
"gb|ACP31303.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum]\n",
|
||||
" Length = 515\n",
|
||||
"\n",
|
||||
"gb|AJE70261.1| nicotinic acetylcholine receptor alpha3 subunit [Apis mellifera]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"emb|CAA04054.1| nicotinic acetylcholine receptor, alpha3 subunit, partial [Locusta migratoria]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"ref|XP_012170034.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_012170035.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_012170036.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_048267067.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"ref|NP_524483.1| nicotinic acetylcholine receptor beta2, isoform A [Drosophila melanogaster] >ref|XP_002032518.2| acetylcholine receptor subunit beta-like 2 [Drosophila sechellia] >ref|XP_002104732.1| acetylcholine receptor subunit beta-like 2 [Drosophila simulans] >ref|XP_033161984.1| acetylcholine receptor subunit beta-like 2 [Drosophila mauritiana] >sp|P25162.3| RecName: Full=Acetylcholine receptor subunit beta-like 2; AltName: Full=Nicotinic acetylcholine receptor beta 2; Flags: Precursor [Drosophila melanogaster] >gb|AAF56304.1| nicotinic acetylcholine receptor beta2, isoform A [Drosophila melanogaster] >gb|EDX14235.1| GD18288 [Drosophila simulans] >gb|KMZ05571.1| uncharacterized protein Dsimw501_GD18288 [Drosophila simulans]\n",
|
||||
" Length = 519\n",
|
||||
"\n",
|
||||
"ref|XP_033202999.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus vancouverensis nearcticus] >ref|XP_033365856.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus vosnesenskii] >ref|XP_043592353.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_043592354.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_043592355.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_043592356.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_048265520.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus terrestris] >ref|XP_050476339.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus huntii] >ref|XP_050600937.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus affinis] >ref|XP_060819514.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pascuorum] >ref|XP_060819517.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pascuorum] >ref|XP_060819518.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pascuorum]\n",
|
||||
" Length = 572\n",
|
||||
"\n",
|
||||
"ref|XP_033365857.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus vosnesenskii] >ref|XP_048265521.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus terrestris] >ref|XP_050476340.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus huntii] >ref|XP_050600938.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus affinis] >ref|XP_060819515.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus pascuorum]\n",
|
||||
" Length = 572\n",
|
||||
"\n",
|
||||
"ref|XP_033202993.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vancouverensis nearcticus] >ref|XP_033202997.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vancouverensis nearcticus] >ref|XP_033202998.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vancouverensis nearcticus] >ref|XP_033365852.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vosnesenskii] >ref|XP_033365853.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vosnesenskii] >ref|XP_033365854.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vosnesenskii] >ref|XP_048265515.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_048265517.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_048265519.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_050476333.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476335.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476336.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476337.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476338.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050600932.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus affinis] >ref|XP_050600935.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus affinis] >ref|XP_050600936.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus affinis]\n",
|
||||
" Length = 583\n",
|
||||
"\n",
|
||||
"ref|XP_033365855.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus vosnesenskii] >ref|XP_048265516.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus terrestris] >ref|XP_050476334.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus huntii] >ref|XP_050600934.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus affinis]\n",
|
||||
" Length = 583\n",
|
||||
"\n",
|
||||
"emb|CAA39211.1| second beta subunit of nicotinic acetylcholine receptor, partial [Drosophila melanogaster] >prf||1701297A nicotinic acetylcholine receptor beta [Drosophila melanogaster]\n",
|
||||
" Length = 500\n",
|
||||
"\n",
|
||||
"ref|NP_001091691.1| nicotinic acetylcholine receptor alpha4 subunit precursor [Apis mellifera] >ref|XP_006562617.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >ref|XP_006562618.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >ref|XP_016768429.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >ref|XP_016768430.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >gb|AAY87892.1| nicotinic acetylcholine receptor alpha4 subunit [Apis mellifera]\n",
|
||||
" Length = 569\n",
|
||||
"\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"blast_record = NCBIXML.read(open(fname))\n",
|
||||
"for alignment in blast_record.alignments:\n",
|
||||
" print(alignment)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"Let's do another blast search for the first protein we had. Again, this can take a long period of time to run on the NCBI servers."
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 13,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"not overwriting file da1_blast.xml\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"da1_seq = None\n",
|
||||
"for record in SeqIO.parse(StringIO(da1), \"fasta\"):\n",
|
||||
" da1_seq = str(record.seq)\n",
|
||||
"\n",
|
||||
"fname = \"da1_blast.xml\"\n",
|
||||
"if not os.path.exists(fname):\n",
|
||||
" result_handle = NCBIWWW.qblast(\"blastp\", \"nr\", da1_seq, entrez_query=taxid_query)\n",
|
||||
" with open(fname, \"w\") as out_handle:\n",
|
||||
" out_handle.write(result_handle.read())\n",
|
||||
"else:\n",
|
||||
" print(\"not overwriting file %s\"%fname)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"In the results, each alignment returns a sequence of HSPS (\"High Scoring Pairs\").\n",
|
||||
"\n",
|
||||
"https://www.ncbi.nlm.nih.gov/books/NBK62051/"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 14,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"ref|NP_001262917.1| nicotinic acetylcholine receptor alpha1, isoform C [Drosophila melanogaster] >ref|NP_524481.2| nicotinic acetylcholine receptor alpha1, isoform A [Drosophila melanogaster] >ref|XP_016952288.1| acetylcholine receptor subunit alpha-like 1 [Drosophila biarmipes] >sp|P09478.2| RecName: Full=Acetylcholine receptor subunit alpha-like 1; AltName: Full=Nicotinic acetylcholine receptor alpha 1; Flags: Precursor [Drosophila melanogaster] >gb|AAF56301.2| nicotinic acetylcholine receptor alpha1, isoform A [Drosophila melanogaster] >gb|AGB96297.1| nicotinic acetylcholine receptor alpha1, isoform C [Drosophila melanogaster]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 3024 (1169 bits), expectation 0.0e+00, alignment length 567\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL 567\n",
|
||||
" MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL\n",
|
||||
"Sbjct: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL 567\n",
|
||||
"\n",
|
||||
"ref|NP_001262916.1| nicotinic acetylcholine receptor alpha1, isoform B [Drosophila melanogaster] >gb|AGB96296.1| nicotinic acetylcholine receptor alpha1, isoform B [Drosophila melanogaster]\n",
|
||||
" Length = 597\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 3020 (1167 bits), expectation 0.0e+00, alignment length 567\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL 567\n",
|
||||
" MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL\n",
|
||||
"Sbjct: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL 567\n",
|
||||
"\n",
|
||||
"emb|CAA30172.1| mature acetylcholine receptor alpha-like subunit [Drosophila melanogaster]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 3014 (1165 bits), expectation 0.0e+00, alignment length 567\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL 567\n",
|
||||
" MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL\n",
|
||||
"Sbjct: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...NTL 567\n",
|
||||
"\n",
|
||||
"ref|NP_001103245.1| nicotinic acetylcholine receptor alpha1 subunit precursor [Tribolium castaneum] >gb|ABS86902.1| nicotinic acetylcholine receptor subunit alpha1 [Tribolium castaneum] >gb|EEZ99265.1| nicotinic acetylcholine receptor subunit alpha1 [Tribolium castaneum]\n",
|
||||
" Length = 545\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 2131 (825 bits), expectation 0.0e+00, alignment length 546\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...GSE 564\n",
|
||||
" N DAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGL+LSQLIDVN... E\n",
|
||||
"Sbjct: 20 GNQDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLKLSQLIDVN...VPE 543\n",
|
||||
"\n",
|
||||
"gb|AHJ11207.1| nicotinic acetylcholine receptor alpha1 variant A [Locusta migratoria]\n",
|
||||
" Length = 570\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 2127 (823 bits), expectation 0.0e+00, alignment length 585\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...GSE 564\n",
|
||||
" MGSVL A V A+ +G ANP+AKRLYDDLLSNYNRLIRPVGN...G E\n",
|
||||
"Sbjct: 1 MGSVLLALVLAAMG-GSGTQANPEAKRLYDDLLSNYNRLIRPVGN...GPE 568\n",
|
||||
"\n",
|
||||
"ref|XP_003397561.2| acetylcholine receptor subunit alpha-like 1 [Bombus terrestris]\n",
|
||||
" Length = 615\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 2122 (822 bits), expectation 0.0e+00, alignment length 609\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFAT--GGLANPDAKRLYDDLLSNYNRLIRPV...GSE 564\n",
|
||||
" +G +L A I+ A G ANP+AKRLYDDLLSNYNRLIRPV...G E\n",
|
||||
"Sbjct: 21 LGGLLAMATAISCLVAPFPGASANPEAKRLYDDLLSNYNRLIRPV...GPE 613\n",
|
||||
"\n",
|
||||
"ref|NP_001091690.1| nicotinic acetylcholine receptor alpha1 subunit [Apis mellifera] >gb|AAY87890.1| nicotinic acetylcholine receptor alpha1 subunit [Apis mellifera] >gb|AJE70259.1| nicotinic acetylcholine receptor alpha1 subunit [Apis mellifera]\n",
|
||||
" Length = 601\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 2109 (816 bits), expectation 0.0e+00, alignment length 602\n",
|
||||
"Query: 18 GGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLI...GSE 564\n",
|
||||
" G AN +AKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLI...G E\n",
|
||||
"Sbjct: 14 GASANSEAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLI...GPE 599\n",
|
||||
"\n",
|
||||
"ref|XP_026298411.1| nicotinic acetylcholine receptor alpha1 subunit isoform X1 [Apis mellifera] >gb|KAG6801309.1| nicotinic acetylcholine receptor alpha1 subunit isoform X1 [Apis mellifera caucasica] >gb|KAG9431275.1| nicotinic acetylcholine receptor alpha1 subunit isoform X1 [Apis mellifera carnica]\n",
|
||||
" Length = 627\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 2108 (816 bits), expectation 0.0e+00, alignment length 621\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFAT--GGLANPDAKRLYDDLLSNYNRLIRPV...GSE 564\n",
|
||||
" +G +L A I+ A G AN +AKRLYDDLLSNYNRLIRPV...G E\n",
|
||||
"Sbjct: 21 LGGLLAMATAISCLVAPFPGASANSEAKRLYDDLLSNYNRLIRPV...GPE 625\n",
|
||||
"\n",
|
||||
"emb|CAA04054.1| nicotinic acetylcholine receptor, alpha3 subunit, partial [Locusta migratoria]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 2019 (782 bits), expectation 0.0e+00, alignment length 555\n",
|
||||
"Query: 33 LSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNLKNQIMTTNVWV...GSE 564\n",
|
||||
" LSNYNRLIRPVGNNSDRLT KMGLRLSQLIDVNLKNQIMTTNVWV...G E\n",
|
||||
"Sbjct: 1 LSNYNRLIRPVGNNSDRLTSKMGLRLSQLIDVNLKNQIMTTNVWV...GPE 538\n",
|
||||
"\n",
|
||||
"gb|AHJ11208.1| nicotinic acetylcholine receptor alpha1 variant B [Locusta migratoria]\n",
|
||||
" Length = 555\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 2017 (781 bits), expectation 0.0e+00, alignment length 586\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...SEN 565\n",
|
||||
" MGSVL A V A+ +G ANP+AKRLYDDLLSNYNRLIRPVGN... E \n",
|
||||
"Sbjct: 1 MGSVLLALVLAAMG-GSGTQANPEAKRLYDDLLSNYNRLIRPVGN...PEE 554\n",
|
||||
"\n",
|
||||
"gb|AHJ11220.1| nicotinic acetylcholine receptor alpha8 variant C [Locusta migratoria]\n",
|
||||
" Length = 574\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1706 (661 bits), expectation 0.0e+00, alignment length 556\n",
|
||||
"Query: 15 FATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLS...AKK 554\n",
|
||||
" T ANPDAKRLYDDLLSNYNRLIRPV NNS+ LTV +GL+LS...+ +\n",
|
||||
"Sbjct: 19 LGTAFEANPDAKRLYDDLLSNYNRLIRPVTNNSETLTVHLGLKLS...SLR 557\n",
|
||||
"\n",
|
||||
"gb|AHJ11221.1| nicotinic acetylcholine receptor alpha8 variant D [Locusta migratoria]\n",
|
||||
" Length = 580\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1705 (661 bits), expectation 0.0e+00, alignment length 547\n",
|
||||
"Query: 15 FATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLS...AKK 554\n",
|
||||
" T ANPDAKRLYDDLLSNYNRLIRPV NNS+ LTV +GL+LS...+ +\n",
|
||||
"Sbjct: 19 LGTAFEANPDAKRLYDDLLSNYNRLIRPVTNNSETLTVHLGLKLS...SLR 563\n",
|
||||
"\n",
|
||||
"gb|AHJ11219.1| nicotinic acetylcholine receptor alpha8 variant B [Locusta migratoria]\n",
|
||||
" Length = 546\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1666 (646 bits), expectation 0.0e+00, alignment length 540\n",
|
||||
"Query: 15 FATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLS...AKK 554\n",
|
||||
" T ANPDAKRLYDDLLSNYNRLIRPV NNS+ LTV +GL+LS...+ +\n",
|
||||
"Sbjct: 19 LGTAFEANPDAKRLYDDLLSNYNRLIRPVTNNSETLTVHLGLKLS...SLR 529\n",
|
||||
"\n",
|
||||
"gb|AHJ11218.1| nicotinic acetylcholine receptor alpha8 variant A [Locusta migratoria]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1665 (645 bits), expectation 0.0e+00, alignment length 540\n",
|
||||
"Query: 15 FATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLS...AKK 554\n",
|
||||
" T ANPDAKRLYDDLLSNYNRLIRPV NNS+ LTV +GL+LS...+ +\n",
|
||||
"Sbjct: 19 LGTAFEANPDAKRLYDDLLSNYNRLIRPVTNNSETLTVHLGLKLS...SLR 523\n",
|
||||
"\n",
|
||||
"emb|CAA04053.1| nicotinic acetylcholine receptor, alpha2 subunit, partial [Locusta migratoria]\n",
|
||||
" Length = 515\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1658 (643 bits), expectation 0.0e+00, alignment length 533\n",
|
||||
"Query: 22 NPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNL...AKK 554\n",
|
||||
" NPDAKRLYDDLLSNYNRLIRPV NNS+ LTV +GL+LSQLI+VNL...+ +\n",
|
||||
"Sbjct: 1 NPDAKRLYDDLLSNYNRLIRPVTNNSETLTVHLGLKLSQLIEVNL...SLR 498\n",
|
||||
"\n",
|
||||
"ref|XP_012170034.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_012170035.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_012170036.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_048267067.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1624 (630 bits), expectation 0.0e+00, alignment length 577\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...KIA 552\n",
|
||||
" M L ++I L +G NPDAKRLYDDLLSNYN+L+RPV N...+IA\n",
|
||||
"Sbjct: 1 MMKSLVGIMWIVLVLISGCSGNPDAKRLYDDLLSNYNKLVRPVVN...EIA 555\n",
|
||||
"\n",
|
||||
"ref|XP_003399573.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus terrestris]\n",
|
||||
" Length = 554\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1620 (628 bits), expectation 0.0e+00, alignment length 569\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...KIA 552\n",
|
||||
" M L ++I L +G NPDAKRLYDDLLSNYN+L+RPV N...+IA\n",
|
||||
"Sbjct: 1 MMKSLVGIMWIVLVLISGCSGNPDAKRLYDDLLSNYNKLVRPVVN...EIA 542\n",
|
||||
"\n",
|
||||
"gb|AJE70261.1| nicotinic acetylcholine receptor alpha3 subunit [Apis mellifera]\n",
|
||||
" Length = 567\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1616 (627 bits), expectation 0.0e+00, alignment length 577\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...KIA 552\n",
|
||||
" M L ++I L +G NPDAKRLYDDLLSNYN+L+RPV N...+IA\n",
|
||||
"Sbjct: 1 MMKSLVGIMWIVLVLISGCSGNPDAKRLYDDLLSNYNKLVRPVVN...EIA 555\n",
|
||||
"\n",
|
||||
"ref|NP_001073029.1| nicotinic acetylcholine receptor alpha3 subunit precursor [Apis mellifera] >ref|XP_016767550.1| nicotinic acetylcholine receptor alpha3 subunit isoform X1 [Apis mellifera] >ref|XP_016767551.1| nicotinic acetylcholine receptor alpha3 subunit isoform X1 [Apis mellifera] >ref|XP_016767552.1| nicotinic acetylcholine receptor alpha3 subunit isoform X1 [Apis mellifera] >gb|KAG6799381.1| nicotinic acetylcholine receptor alpha3 subunit precursor [Apis mellifera caucasica] >gb|KAG9433524.1| nicotinic acetylcholine receptor alpha3 subunit precursor [Apis mellifera carnica] >gb|AAY87891.1| nicotinic acetylcholine receptor alpha3 subunit [Apis mellifera]\n",
|
||||
" Length = 566\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1613 (625 bits), expectation 0.0e+00, alignment length 575\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...KIA 552\n",
|
||||
" M L ++I L +G NPDAKRLYDDLLSNYN+L+RPV N...+IA\n",
|
||||
"Sbjct: 1 MMKSLVGIMWIVLVLISGCSGNPDAKRLYDDLLSNYNKLVRPVVN...EIA 554\n",
|
||||
"\n",
|
||||
"ref|NP_001107770.1| nicotinic acetylcholine receptor alpha 3 subunit precursor [Tribolium castaneum] >ref|XP_008200302.1| PREDICTED: nicotinic acetylcholine receptor alpha 3 subunit isoform X1 [Tribolium castaneum] >gb|ABS86904.1| nicotinic acetylcholine receptor subunit alpha3 [Tribolium castaneum] >gb|ABV72695.1| nicotinic acetylcholine receptor alpha 3 subunit [Tribolium castaneum] >gb|ACM09844.1| nicotinic acetylcholine receptor subunit a3 [Tribolium castaneum] >gb|EEZ97689.1| nicotinic acetylcholine receptor subunit alpha3 [Tribolium castaneum]\n",
|
||||
" Length = 551\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1612 (625 bits), expectation 0.0e+00, alignment length 555\n",
|
||||
"Query: 5 LFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDR...KIA 552\n",
|
||||
" L ++I L +G NPDAKRLYDDLLSNYN+L+RPV N SD ...+IA\n",
|
||||
"Sbjct: 4 LVGIMWIVLVLISGCSGNPDAKRLYDDLLSNYNKLVRPVVNVSDA...EIA 539\n",
|
||||
"\n",
|
||||
"gb|KAG6799677.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera caucasica] >gb|KAG9434134.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera carnica]\n",
|
||||
" Length = 534\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1610 (624 bits), expectation 0.0e+00, alignment length 562\n",
|
||||
"Query: 1 MGSVLFAAVFIALH--FATGGL----ANPDAKRLYDDLLSNYNRL...KKF 556\n",
|
||||
" M + +F LH ++ GL ANPD KRLYDDLLSNYNRL...+ +\n",
|
||||
"Sbjct: 1 MQILTLGVLFNTLHIIYSVAGLKIFEANPDTKRLYDDLLSNYNRL...RNY 523\n",
|
||||
"\n",
|
||||
"ref|XP_016767553.1| nicotinic acetylcholine receptor alpha3 subunit isoform X2 [Apis mellifera]\n",
|
||||
" Length = 553\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1610 (624 bits), expectation 0.0e+00, alignment length 567\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGN...KIA 552\n",
|
||||
" M L ++I L +G NPDAKRLYDDLLSNYN+L+RPV N...+IA\n",
|
||||
"Sbjct: 1 MMKSLVGIMWIVLVLISGCSGNPDAKRLYDDLLSNYNKLVRPVVN...EIA 541\n",
|
||||
"\n",
|
||||
"ref|NP_001011575.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera] >gb|AAM51823.1| neuronal nicotinic acetylcholine receptor alpha-3 [Apis mellifera] >gb|AJE70266.1| nicotinic acetylcholine receptor alpha8 subunit [Apis mellifera]\n",
|
||||
" Length = 537\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1608 (624 bits), expectation 0.0e+00, alignment length 562\n",
|
||||
"Query: 1 MGSVLFAAVFIALH--FATGGL----ANPDAKRLYDDLLSNYNRL...KKF 556\n",
|
||||
" M + +F LH ++ GL ANPD KRLYDDLLSNYNRL...+ +\n",
|
||||
"Sbjct: 4 MQILTLGVLFNTLHIIYSVAGLKIFEANPDTKRLYDDLLSNYNRL...RNY 526\n",
|
||||
"\n",
|
||||
"ref|XP_012163744.1| acetylcholine receptor subunit beta-like 2 isoform X1 [Bombus terrestris] >ref|XP_050590207.1| acetylcholine receptor subunit beta-like 2 isoform X1 [Bombus affinis]\n",
|
||||
" Length = 535\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1607 (623 bits), expectation 0.0e+00, alignment length 562\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGL------ANPDAKRLYDDLLSNYNRL...KKF 556\n",
|
||||
" M + F+ +F LH G + ANPD KRLYDDLLSNYNRL...+ +\n",
|
||||
"Sbjct: 1 MRILTFSILFNVLHIIFGAIGLKIYEANPDTKRLYDDLLSNYNRL...RNY 523\n",
|
||||
"\n",
|
||||
"ref|XP_026296304.1| nicotinic acetylcholine receptor alpha8 subunit isoform X1 [Apis mellifera]\n",
|
||||
" Length = 533\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1602 (621 bits), expectation 0.0e+00, alignment length 562\n",
|
||||
"Query: 1 MGSVLFAAVFIALH--FATGGL----ANPDAKRLYDDLLSNYNRL...KKF 556\n",
|
||||
" M + +F LH ++ GL ANPD KRLYDDLLSNYNRL...+ +\n",
|
||||
"Sbjct: 4 MQILTLGVLFNTLHIIYSVAGLKIFEANPDTKRLYDDLLSNYNRL...RNY 522\n",
|
||||
"\n",
|
||||
"ref|XP_033202999.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus vancouverensis nearcticus] >ref|XP_033365856.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus vosnesenskii] >ref|XP_043592353.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_043592354.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_043592355.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_043592356.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pyrosoma] >ref|XP_048265520.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus terrestris] >ref|XP_050476339.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus huntii] >ref|XP_050600937.1| acetylcholine receptor subunit alpha-like isoform X3 [Bombus affinis] >ref|XP_060819514.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pascuorum] >ref|XP_060819517.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pascuorum] >ref|XP_060819518.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus pascuorum]\n",
|
||||
" Length = 572\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1598 (620 bits), expectation 0.0e+00, alignment length 556\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KIA 552\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...+ A\n",
|
||||
"Sbjct: 18 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...EFA 562\n",
|
||||
"\n",
|
||||
"ref|NP_001103419.1| nicotinic acetylcholine receptor alpha 8 subunit isoform 2 precursor [Tribolium castaneum] >gb|ABS86912.1| nicotinic acetylcholine receptor subunit alpha8 [Tribolium castaneum]\n",
|
||||
" Length = 508\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1597 (619 bits), expectation 0.0e+00, alignment length 529\n",
|
||||
"Query: 19 GLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLID...PID 545\n",
|
||||
" +ANPDAKRLYDDLLSNYNRLIRPV N++ LTV +GL++SQLI+...P+D\n",
|
||||
"Sbjct: 20 NIANPDAKRLYDDLLSNYNRLIRPVENHTQTLTVWLGLKISQLIE...PVD 502\n",
|
||||
"\n",
|
||||
"ref|XP_012163745.1| acetylcholine receptor subunit beta-like 2 isoform X2 [Bombus terrestris] >ref|XP_050590208.1| acetylcholine receptor subunit beta-like 2 isoform X2 [Bombus affinis]\n",
|
||||
" Length = 531\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1597 (619 bits), expectation 0.0e+00, alignment length 562\n",
|
||||
"Query: 1 MGSVLFAAVFIALHFATGGL------ANPDAKRLYDDLLSNYNRL...KKF 556\n",
|
||||
" M + F+ +F LH G + ANPD KRLYDDLLSNYNRL...+ +\n",
|
||||
"Sbjct: 1 MRILTFSILFNVLHIIFGAIGLKIYEANPDTKRLYDDLLSNYNRL...RNY 519\n",
|
||||
"\n",
|
||||
"gb|KYB29426.1| nicotinic acetylcholine receptor subunit alpha11 [Tribolium castaneum]\n",
|
||||
" Length = 491\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1595 (619 bits), expectation 0.0e+00, alignment length 529\n",
|
||||
"Query: 19 GLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLID...PID 545\n",
|
||||
" +ANPDAKRLYDDLLSNYNRLIRPV N++ LTV +GL++SQLI+...P+D\n",
|
||||
"Sbjct: 3 NIANPDAKRLYDDLLSNYNRLIRPVENHTQTLTVWLGLKISQLIE...PVD 485\n",
|
||||
"\n",
|
||||
"ref|NP_001155998.1| nicotinic acetylcholine receptor alpha 8 subunit isoform 1 precursor [Tribolium castaneum] >gb|ACP31302.1| nicotinic acetylcholine receptor a8 subunit splice variant [Tribolium castaneum] >gb|ACP31304.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum] >gb|ACP31305.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum] >gb|ACP31306.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum]\n",
|
||||
" Length = 515\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1594 (618 bits), expectation 0.0e+00, alignment length 527\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...PID 545\n",
|
||||
" ANPDAKRLYDDLLSNYNRLIRPV N++ LTV +GL++SQLI++N...P+D\n",
|
||||
"Sbjct: 29 ANPDAKRLYDDLLSNYNRLIRPVENHTQTLTVWLGLKISQLIEMN...PVD 509\n",
|
||||
"\n",
|
||||
"gb|KYB29425.1| nicotinic acetylcholine receptor subunit alpha11 [Tribolium castaneum]\n",
|
||||
" Length = 498\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1592 (617 bits), expectation 0.0e+00, alignment length 527\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...PID 545\n",
|
||||
" ANPDAKRLYDDLLSNYNRLIRPV N++ LTV +GL++SQLI++N...P+D\n",
|
||||
"Sbjct: 12 ANPDAKRLYDDLLSNYNRLIRPVENHTQTLTVWLGLKISQLIEMN...PVD 492\n",
|
||||
"\n",
|
||||
"ref|NP_524482.1| nicotinic acetylcholine receptor alpha2, isoform A [Drosophila melanogaster] >ref|NP_733001.1| nicotinic acetylcholine receptor alpha2, isoform B [Drosophila melanogaster] >ref|XP_002032516.1| acetylcholine receptor subunit alpha-like 2 [Drosophila sechellia] >ref|XP_002104730.1| acetylcholine receptor subunit alpha-like 2 [Drosophila simulans] >ref|XP_033165329.1| acetylcholine receptor subunit alpha-like 2 [Drosophila mauritiana] >sp|P17644.1| RecName: Full=Acetylcholine receptor subunit alpha-like 2; AltName: Full=Nicotinic acetylcholine receptor alpha 2; Flags: Precursor [Drosophila melanogaster] >gb|ACL85307.1| nAcRalpha-96Ab-PA, partial [synthetic construct] >gb|AAF56302.2| nicotinic acetylcholine receptor alpha2, isoform A [Drosophila melanogaster] >gb|AAF56303.1| nicotinic acetylcholine receptor alpha2, isoform B [Drosophila melanogaster] >gb|AAL13675.1| GH22843p [Drosophila melanogaster] >gb|ACL90211.1| nAcRalpha-96Ab-PA [synthetic construct]\n",
|
||||
" Length = 576\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1591 (617 bits), expectation 0.0e+00, alignment length 547\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...FEL 558\n",
|
||||
" ANPDAKRLYDDLLSNYNRLIRPV NN+D + VK+GLRLSQLID+N...+ L\n",
|
||||
"Sbjct: 41 ANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLN...YNL 571\n",
|
||||
"\n",
|
||||
"ref|XP_033202993.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vancouverensis nearcticus] >ref|XP_033202997.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vancouverensis nearcticus] >ref|XP_033202998.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vancouverensis nearcticus] >ref|XP_033365852.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vosnesenskii] >ref|XP_033365853.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vosnesenskii] >ref|XP_033365854.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus vosnesenskii] >ref|XP_048265515.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_048265517.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_048265519.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus terrestris] >ref|XP_050476333.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476335.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476336.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476337.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050476338.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus huntii] >ref|XP_050600932.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus affinis] >ref|XP_050600935.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus affinis] >ref|XP_050600936.1| acetylcholine receptor subunit alpha-like isoform X1 [Bombus affinis]\n",
|
||||
" Length = 583\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1588 (616 bits), expectation 0.0e+00, alignment length 567\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KIA 552\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...+ A\n",
|
||||
"Sbjct: 18 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...EFA 573\n",
|
||||
"\n",
|
||||
"gb|KYB29325.1| nicotinic acetylcholine receptor subunit alpha4 [Tribolium castaneum]\n",
|
||||
" Length = 598\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1586 (615 bits), expectation 0.0e+00, alignment length 559\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KFE 557\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...KFE\n",
|
||||
"Sbjct: 59 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...KFE 584\n",
|
||||
"\n",
|
||||
"ref|NP_001091691.1| nicotinic acetylcholine receptor alpha4 subunit precursor [Apis mellifera] >ref|XP_006562617.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >ref|XP_006562618.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >ref|XP_016768429.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >ref|XP_016768430.1| nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Apis mellifera] >gb|AAY87892.1| nicotinic acetylcholine receptor alpha4 subunit [Apis mellifera]\n",
|
||||
" Length = 569\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1586 (615 bits), expectation 0.0e+00, alignment length 550\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...PID 545\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...PID\n",
|
||||
"Sbjct: 17 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...PID 552\n",
|
||||
"\n",
|
||||
"ref|NP_001103246.1| nicotinic acetylcholine receptor alpha4 subunit isoform 1 precursor [Tribolium castaneum] >ref|XP_044259329.1| acetylcholine receptor subunit alpha-like isoform X3 [Tribolium madens] >gb|ABS86905.1| nicotinic acetylcholine receptor subunit alpha4 variant [Tribolium castaneum] >gb|ACM09852.1| nicotinic acetylcholine receptor subunit a4 [Tribolium castaneum]\n",
|
||||
" Length = 556\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1586 (615 bits), expectation 0.0e+00, alignment length 559\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KFE 557\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...KFE\n",
|
||||
"Sbjct: 17 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...KFE 542\n",
|
||||
"\n",
|
||||
"ref|XP_008201498.1| PREDICTED: nicotinic acetylcholine receptor alpha4 subunit isoform X1 [Tribolium castaneum] >ref|XP_044259327.1| acetylcholine receptor subunit alpha-like isoform X1 [Tribolium madens]\n",
|
||||
" Length = 560\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1584 (614 bits), expectation 0.0e+00, alignment length 563\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KFE 557\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...KFE\n",
|
||||
"Sbjct: 17 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...KFE 546\n",
|
||||
"\n",
|
||||
"ref|XP_033365857.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus vosnesenskii] >ref|XP_048265521.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus terrestris] >ref|XP_050476340.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus huntii] >ref|XP_050600938.1| acetylcholine receptor subunit alpha-like isoform X4 [Bombus affinis] >ref|XP_060819515.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus pascuorum]\n",
|
||||
" Length = 572\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1579 (612 bits), expectation 0.0e+00, alignment length 556\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KIA 552\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...+ A\n",
|
||||
"Sbjct: 18 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...EFA 562\n",
|
||||
"\n",
|
||||
"gb|ACP31303.1| nicotinic acetylcholine receptor a8 subunit [Tribolium castaneum]\n",
|
||||
" Length = 515\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1579 (612 bits), expectation 0.0e+00, alignment length 527\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...PID 545\n",
|
||||
" ANPDAKRLYDDLLSNYNRLIRPV N++ LTV +GL++SQLI++N...P+D\n",
|
||||
"Sbjct: 29 ANPDAKRLYDDLLSNYNRLIRPVENHTQTLTVWLGLKISQLIEMN...PVD 509\n",
|
||||
"\n",
|
||||
"ref|XP_003397559.1| acetylcholine receptor subunit alpha-L1 isoform X2 [Bombus terrestris]\n",
|
||||
" Length = 541\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1576 (611 bits), expectation 0.0e+00, alignment length 556\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...KKF 556\n",
|
||||
" +NPDAKRLYDDLLSNYNRLIRPV NN+D + VK+GLRLSQLID+N...++F\n",
|
||||
"Sbjct: 17 SNPDAKRLYDDLLSNYNRLIRPVSNNNDTVVVKLGLRLSQLIDLN...QQF 530\n",
|
||||
"\n",
|
||||
"gb|AHJ11209.1| nicotinic acetylcholine receptor alpha2 [Locusta migratoria]\n",
|
||||
" Length = 551\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1575 (611 bits), expectation 0.0e+00, alignment length 541\n",
|
||||
"Query: 22 NPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVNL...KKF 556\n",
|
||||
" NPDAKRLYDDLLSNYNRLIRPV NN+D + VK+GLRLSQLID+NL...++F\n",
|
||||
"Sbjct: 25 NPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNL...QQF 545\n",
|
||||
"\n",
|
||||
"ref|NP_001011625.1| nicotinic acetylcholine receptor alpha2 subunit precursor [Apis mellifera] >ref|XP_006561565.1| nicotinic acetylcholine receptor alpha2 subunit isoform X1 [Apis mellifera] >ref|XP_026298380.1| nicotinic acetylcholine receptor alpha2 subunit isoform X1 [Apis mellifera] >gb|KAG6801311.1| nicotinic acetylcholine receptor alpha2 subunit precursor [Apis mellifera caucasica] >gb|KAG9431277.1| nicotinic acetylcholine receptor alpha2 subunit precursor [Apis mellifera carnica] >gb|AAS48080.1| neuronal nicotinic acetylcholine receptor Apisa2 subunit [Apis mellifera] >gb|AJE70260.1| nicotinic acetylcholine receptor alpha2 subunit [Apis mellifera]\n",
|
||||
" Length = 541\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1575 (611 bits), expectation 0.0e+00, alignment length 550\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...KKF 556\n",
|
||||
" NPDAKRLYDDLLSNYNRLIRPV NN+D + VK+GLRLSQLID+N...++F\n",
|
||||
"Sbjct: 17 GNPDAKRLYDDLLSNYNRLIRPVSNNNDTVVVKLGLRLSQLIDLN...QQF 530\n",
|
||||
"\n",
|
||||
"ref|XP_012166790.1| acetylcholine receptor subunit alpha-L1 isoform X1 [Bombus terrestris]\n",
|
||||
" Length = 544\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1572 (610 bits), expectation 0.0e+00, alignment length 559\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...KKF 556\n",
|
||||
" +NPDAKRLYDDLLSNYNRLIRPV NN+D + VK+GLRLSQLID+N...++F\n",
|
||||
"Sbjct: 17 SNPDAKRLYDDLLSNYNRLIRPVSNNNDTVVVKLGLRLSQLIDLN...QQF 533\n",
|
||||
"\n",
|
||||
"ref|XP_033365855.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus vosnesenskii] >ref|XP_048265516.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus terrestris] >ref|XP_050476334.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus huntii] >ref|XP_050600934.1| acetylcholine receptor subunit alpha-like isoform X2 [Bombus affinis]\n",
|
||||
" Length = 583\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1569 (608 bits), expectation 0.0e+00, alignment length 567\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KIA 552\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...+ A\n",
|
||||
"Sbjct: 18 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...EFA 573\n",
|
||||
"\n",
|
||||
"ref|XP_006562616.1| nicotinic acetylcholine receptor alpha4 subunit isoform X2 [Apis mellifera] >gb|AAY87893.1| nicotinic acetylcholine receptor alpha4 subunit [Apis mellifera] >gb|AJE70262.1| nicotinic acetylcholine receptor alpha4 subunit [Apis mellifera]\n",
|
||||
" Length = 569\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1568 (608 bits), expectation 0.0e+00, alignment length 550\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...PID 545\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...PID\n",
|
||||
"Sbjct: 17 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...PID 552\n",
|
||||
"\n",
|
||||
"ref|NP_001155997.1| nicotinic acetylcholine receptor alpha4 subunit isoform 2 precursor [Tribolium castaneum] >ref|XP_044259330.1| acetylcholine receptor subunit alpha-like isoform X4 [Tribolium madens] >gb|ABS86906.1| nicotinic acetylcholine receptor subunit alpha4 variant [Tribolium castaneum]\n",
|
||||
" Length = 556\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1567 (608 bits), expectation 0.0e+00, alignment length 559\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KFE 557\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...KFE\n",
|
||||
"Sbjct: 17 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...KFE 542\n",
|
||||
"\n",
|
||||
"emb|CAB77445.1| nicotinic acetylcholine receptor Dalpha 4 subunit [Drosophila melanogaster]\n",
|
||||
" Length = 568\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1567 (608 bits), expectation 0.0e+00, alignment length 551\n",
|
||||
"Query: 2 GSVLFAAVFIALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNN...QPI 544\n",
|
||||
" G L A + AL NPDAKRLYDDLLSNYN+L+RPV N ... PI\n",
|
||||
"Sbjct: 18 GGTLRAWILSALMVHGAVAGNPDAKRLYDDLLSNYNKLVRPVVNT...IPI 548\n",
|
||||
"\n",
|
||||
"ref|NP_001103423.1| nicotinic acetylcholine receptor alpha 2 subunit precursor [Tribolium castaneum] >gb|ABS86903.1| nicotinic acetylcholine receptor subunit alpha2 [Tribolium castaneum] >gb|EFA10793.1| nicotinic acetylcholine receptor subunit alpha2 [Tribolium castaneum]\n",
|
||||
" Length = 541\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1566 (607 bits), expectation 0.0e+00, alignment length 536\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...KKF 556\n",
|
||||
" NPDAKRLYDDLLSNYNRLIRPV NN+D + VK+GLRLSQLI++N...++F\n",
|
||||
"Sbjct: 21 TNPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIELN...QQF 535\n",
|
||||
"\n",
|
||||
"gb|ACM09847.1| nicotinic acetylcholine receptor subunit a2 [Tribolium castaneum] >gb|ACM09848.1| nicotinic acetylcholine receptor subunit a2 [Tribolium castaneum] >gb|ACM09849.1| nicotinic acetylcholine receptor subunit a2 [Tribolium castaneum]\n",
|
||||
" Length = 540\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1566 (607 bits), expectation 0.0e+00, alignment length 536\n",
|
||||
"Query: 21 ANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMGLRLSQLIDVN...KKF 556\n",
|
||||
" NPDAKRLYDDLLSNYNRLIRPV NN+D + VK+GLRLSQLI++N...++F\n",
|
||||
"Sbjct: 20 TNPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIELN...QQF 534\n",
|
||||
"\n",
|
||||
"gb|EEZ99194.2| nicotinic acetylcholine receptor subunit alpha4 [Tribolium castaneum]\n",
|
||||
" Length = 598\n",
|
||||
"\n",
|
||||
"1 HSPs\n",
|
||||
"Score 1565 (607 bits), expectation 0.0e+00, alignment length 559\n",
|
||||
"Query: 11 IALHFATGGLANPDAKRLYDDLLSNYNRLIRPVGNNSDRLTVKMG...KFE 557\n",
|
||||
" + +H A G NPDAKRLYDDLLSNYN+L+RPV N SD L V + ...KFE\n",
|
||||
"Sbjct: 59 LVVHGAVAG--NPDAKRLYDDLLSNYNKLVRPVVNTSDVLRVCIK...KFE 584\n",
|
||||
"\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"blast_record = NCBIXML.read(open(fname))\n",
|
||||
"for alignment in blast_record.alignments:\n",
|
||||
" print(alignment)\n",
|
||||
" print(\"%d HSPs\"%len(alignment.hsps))\n",
|
||||
" for hsps in alignment.hsps:\n",
|
||||
" print(hsps)\n",
|
||||
" print()"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"celltoolbar": "Create Assignment",
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3 (ipykernel)",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.11.7"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 4
|
||||
}
|
||||
Loading…
Reference in a new issue