1. Casey Dunn
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agalma / Subsetting swissprot

Subsetting swissprot

Assumes you are in a directory with the full swissprot database. You can get the full swissport database here.

metazoa

Download the GI list from http://www.ncbi.nlm.nih.gov/protein/?term=txid33208[Organism:exp] by clicking on "Send to" -> "File" -> "Format: GI List" -> "Create file". Move the downloaded file sequence.gi.txt to the path gilists/metazoa.txt in the working dir.

cd gilists
blastdb_aliastool -gi_file_in metazoa.txt -gi_file_out metazoa.gil
cd ..
blastdb_aliastool -out swissprot.metazoa.alias -gilist gilists/metazoa.gil -db swissprot -dbtype prot
blastdbcmd -db swissprot.metazoa.alias -entry all | makeblastdb -out swissprot.metazoa -title "Non-redundant UniProtKB/SwissProt sequences (metazoa subset)" -dbtype prot
rm swissprot.metazoa.alias.pal

viridiplantae

Download the GI list from http://www.ncbi.nlm.nih.gov/protein/?term=txid33090[Organism:exp] by clicking on "Send to" -> "File" -> "Format: GI List" -> "Create file". Move the downloaded file sequence.gi.txt to the path gilists/viridiplantae.txt in the working dir.

cd gilists
blastdb_aliastool -gi_file_in viridiplantae.txt -gi_file_out viridiplantae.gil
cd ..
blastdb_aliastool -out swissprot.viridiplantae.alias -gilist gilists/viridiplantae.gil -db swissprot -dbtype prot
blastdbcmd -db swissprot.viridiplantae.alias -entry all | makeblastdb -out swissprot.viridiplantae -title "Non-redundant UniProtKB/SwissProt sequences (viridiplantae subset)" -dbtype prot
rm swissprot.viridiplantae.alias.pal

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