How to retrieve accession from Uniprot?
1
1
Entering edit mode
4.5 years ago
Learner ▴ 250

I have a bunch of sequenes and i want to get their Uniprot accession number.

Is there any way to do them automatically rather than doing them one by one?

Genome proteome R Uniport • 1.2k views
ADD COMMENT
2
Entering edit mode

Not if you only have sequences. You would have to do BLAST @Uniprot to first identify what they are to get that information.

ADD REPLY
0
Entering edit mode

@genomax I thought so, is there any automatic way to do the blast for a bunch of protein in your opinion ? I googled it already but the stuff did not lead me to anything

ADD REPLY
2
Entering edit mode

You could download uniprot sequences and then create a blast index locally to search against. I am not sure if NCBI command line blastp --remote allows you to search against Uniprot db (called swissprot) that is present in web version? That would be another option.

ADD REPLY
1
Entering edit mode
4.5 years ago
c.chakraborty ▴ 170

Hey if you have a set of amino acid sequences you can copy them on Uniprot- Peptide search, each sequence separated by line, also identify the species you are investigating, and you will retrieve their names, Uniprot id.

ADD COMMENT

Login before adding your answer.

Traffic: 1670 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