retrieve organism from protein list

Question

[Assa Yeroslaviz]

Hi,

I have a list of proteins accumulated from a BLAT search against nr. I would like to know how I can retrieve the organism each of the proteins belongs to.

thanks in advance

Assa

Answer 1

[shenwei356]

Target proteins from nr should have accesion id or gi, so

1. Mapping accession id or gi to taxid using prot.accession2taxid.gz. csvtk is used for grepping given columns.

   $ zcat prot.accession2taxid.gz
   accession       accession.version       taxid   gi
   P29373  P29373.2        9606    132401
   P22935  P22935.2        10090   132402
   P18902  P18902.1        9913    132403
   
   # using accession
   $ zcat prot.accession2taxid.gz | csvtk -t grep -f accession -P acc.txt | cut -f 3 | sed 1d > taxid.txt
   
   # using gi
   $ zcat prot.accession2taxid.gz | csvtk -t grep -f gi -P gi.txt | cut -f 3 | sed 1d > taxid.txt
   

2. Retrieving organism information with the taxid using tools like ete3 (How to get phylum, class etc taxonomic ids from taxid? ), or taxonkit