Retrieve Protein Sequences from Uniprot
1
0
Entering edit mode
20 months ago

I have a list of protein id's, these all traceback to Uniprot. However, I wanted to know if I can obtain sequence information from these proteins from uniprot protein ids.. Is there any package in biopython to do this?

I found this snippet of code online and it does give the sequence information but not sure if there is a better way

import requests as r from Bio import SeqIO from io import StringIO

cID='A0A061AD41'

baseUrl="http://www.uniprot.org/uniprot/" currentUrl=baseUrl+cID+".fasta" response = r.post(currentUrl) cData=''.join(response.text)

Seq=StringIO(cData) pSeq=list(SeqIO.parse(Seq,'fasta'))

where pSeq prints:

[SeqRecord(seq=Seq('MQAALIGLNFPLQRRFLSGVLTTTSSAKRCYSGDTGKPYDCTSAEHKKELEECY...SSS', SingleLetterAlphabet()), id='sp|O45228|PROD_CAEEL', name='sp|O45228|PROD_CAEEL', description='sp|O45228|PROD_CAEEL Proline dehydrogenase 1, mitochondrial OS=Caenorhabditis elegans OX=6239 GN=prdh-1 PE=2 SV=2', dbxrefs=[])]
sequence python biopython uniprot • 665 views
ADD COMMENT
1
Entering edit mode
20 months ago
Shalu Jhanwar ▴ 500

Have a look at the previous post here showing retrieval of the sequences from UniProt protein Ids.

ADD COMMENT
0
Entering edit mode

I saw that this uses linux command directly, was curious if I could do it directly from a python command.

ADD REPLY

Login before adding your answer.

Traffic: 863 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6