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Getting full protein names from Uniprot-Swissprot identifiers or short names

Hello,

I have a list of Uniprot/swissprot identifiers, such as:

P12281 Q05397 P50430 P54904 ...

I also have the short names for the corresponding identifiers :

MOEA_ECOLI FAK1_HUMAN ARSB_RAT P5CR1_ARATH ...

Does anyone knows how can I get the full protein names for these proteins in batch?, like the first one would be: Molybdopterin molybdenumtransferase

If I could get even more information in this entry, like the associated GO terms, even better...

thank you!

swissprot uniprot protein names go terms
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updated by Denise CS Denise CS • written by lay_0 lay_0

3 answers

Try the Retrieve/ID mapping tool from UniProt. MOEA_ECOLI FAK1_HUMAN ARSB_RAT P5CR1_ARATH will be your 'UniProtKB AC/ID' and if you choose UniProtKB you will get a table with the protein names. You can filter the results by Gene Ontology, Taxonomy and others.

• 0 views • link
written by Denise CS Denise CS

There will be a more clever way (or a single file of ID mapping somewhere) of doing this but here is one you can use now.

  1. Get the uniprot fasta sequences here.
  2. Unzip the file by gunzip uniprot_sprot.fasta.gz
  3. Collect all fasta headers in a new file grep "^>" uniprot_sprot.fasta > uniprot_header
  4. Pull the names out that you need e.g. grep FAK1_HUMAN uniprot_header
  5. Parse as needed
  6. You can iterate over your ID's to get them all.
• 0 views • link
written by GenoMax GenoMax

Thanks, that should work too, but I didn't want to go back to the sequences in the database. I was being a bit stubborn about trying the gene id conversion tool before because I didn't really want to "convert IDs"... but after natasha posted I decided to try, and it seems to work just fine, it gives me the full protein names.

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written by lay_0 lay_0

Which of the "conversion tools" did you use? There are multiple in that thread and some are not being currently maintained (e.g. DAVID)

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written by GenoMax GenoMax

In DAVID webpage I "converted" from Uniprot_ID to David(Default), and it gave a list of full names for the proteins when I tried with a small subset. However it didn't work with my whole list (returns an empty table). I just tried Denise suggestion and that was much better as the result it is in the same Uniprot database. Thank you.

• 0 views • link
written by lay_0 lay_0

See this post:

Gene Id Conversion Tool

See also this post

How To Programmatically Retrieve A Batch Of Fasta Sequences From For A List Of Uniprot Accession Ids?

There are Perl-versions and UniProt-batch version inside.

• 0 views • link
written by natasha.sernova natasha.sernova

the conversion tool works for my purpose, thanks!

I recall, it does;t work for my full list, only for a small subset, I don't know what is going on.

• 0 views • link
written by lay_0 lay_0

DAVID is not being actively maintained. Last updates were probably from 2010-2011. So it is not surprising.

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written by GenoMax GenoMax

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