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Question: Uniprot Accession and Position to peptide sequence
0
gravatar for desc
3.5 years ago by
desc • 0
desc • 0 wrote:

I have a data frame of Uniprot Accessions and amino acid positions within each represented protein. I would like to extract a peptide of some length (lets say +/- 5 amino acids, total length of 11 residues), from Uniprot surrounding each position.

Example: Accession_position: P02699_311 Result: YIMMNKQFRNC

I've seen similar posts, but no solutions pertaining to solving this issue. Does anyone have hints for where to look to solve this, or better yet a solution already?
peptide uniprot R • 998 views
ADD COMMENT • link •
modified 3.5 years ago by Elisabeth Gasteiger • 1.7k • written 3.5 years ago by desc • 0
2
gravatar for Jean-Karim Heriche
3.5 years ago by
Jean-Karim Heriche ♦ 21k
EMBL Heidelberg, Germany
Jean-Karim Heriche ♦ 21k wrote:

Try:

use strict;
use warnings;
use Bio::DB::SwissProt;

my $pos = 311;
my $gb = new Bio::DB::SwissProt(); 
my $seqObj = $gb->get_Seq_by_id('P02699');
my $seq = $seqObj->seq();
my $peptide = substr($seq,$pos-6,11);
ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by Jean-Karim Heriche ♦ 21k

Thanks! We ended up using a C script, but this worked well, and could be adapted with a for loop to run over a larger file.

ADD REPLY • link written 3.5 years ago by desc • 0
0
gravatar for Elisabeth Gasteiger
3.5 years ago by
Elisabeth Gasteiger • 1.7k
Geneva
Elisabeth Gasteiger • 1.7k wrote:

You have solved your problem, but just in case it may be useful for others: You could write a script to transform your "identifiers" from P02699_311 to P02699[306-316] and then submit the resulting lists to the batch retrieve service on the UniProt website, http://www.uniprot.org/uploadlists

You can download the results in various formats, including FASTA (select "source list"), which looks like this:

>sp|P02699|306-316
YIMMNKQFRNC
>sp|P02699|308-318
MMNKQFRNCMV
>sp|P02699|309-319
MNKQFRNCMVT
ADD COMMENT • link written 3.5 years ago by Elisabeth Gasteiger • 1.7k
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