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retrieve organism from protein list

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

proteom rna-seq blast
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updated by shenwei356 shenwei356 • written by Assa Yeroslaviz Assa Yeroslaviz

1 answer

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

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written by shenwei356 shenwei356

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