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Swiss-Prot Id check

Hello,

I have huge file of protein IDs and I need to check them if they are swiss-prot ids? Do you have any suggestion for me?

Thank you.

protein swiss-prot
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written by trumbia • trumbia

Please list a few of the IDs that you have. Thank you.

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written by Kevin Blighe Kevin Blighe

Yes, well, they appear to be UniProt; however, the species are mixed, as I see human, mouse, and rat IDs. What do you need to do with these?; from where did you obtain them? Thank you!

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written by Kevin Blighe Kevin Blighe

Ah! Mensur answered! See below.

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written by Kevin Blighe Kevin Blighe

2 answers

You could use UniProt ID converter. Paste your ID's and map.

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written by GenoMax GenoMax

This is a crude way, but it should work.

Download and unpack Swiss-Prot:

wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

gunzip uniprot_sprot.fasta.gz

Save your IDs into a file, say ID.txt. I did so for the 5 ID numbers you provided. Then simply (f)grep your ID file against the database, and either count the hits or save them in a file.

Counting:

fgrep -f ID.txt uniprot_sprot.fasta | wc -l

It counts 3 matches.

Printing the output:

fgrep -f ID.txt uniprot_sprot.fasta

>sp|Q8C050|KS6A5_MOUSE Ribosomal protein S6 kinase alpha-5 OS=Mus musculus OX=10090 GN=Rps6ka5 PE=1 SV=2
>sp|P47811|MK14_MOUSE Mitogen-activated protein kinase 14 OS=Mus musculus OX=10090 GN=Mapk14 PE=1 SV=3
>sp|Q15672|TWST1_HUMAN Twist-related protein 1 OS=Homo sapiens OX=9606 GN=TWIST1 PE=1 SV=1
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written by Mensur Dlakic Mensur Dlakic

Thank you for your help.

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written by trumbia • trumbia

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