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Downloading from nr data base.

Dear all

I would like to download the genes information for the streptomyces genus from the nr database. I tried to do it but I downloaded all the database. Could someone explain me how to filter out the data to only get the information for streptomyces?

Thanks

Carlos

gene
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updated by Jake Warner Jake Warner • written by Carlos Caicedo Carlos Caicedo

2 answers

You could try using blastdbcmd:

blastdbcmd -db /scratch/db/nr/blastDB/nr -dbtype prot -entry all -outfmt "%g %T" | \
awk ' { if ($2 == 1883) { print $1 } } ' | \
blastdbcmd -db /scratch/db/nr/blastDB/nr -dbtype prot -entry_batch - -out streptomyces.txt

I think 1883 is the taxid for all streptomyces...

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written by Jake Warner Jake Warner

Just use a tool that indexes and parses the FASTA format, and allows for a case-insensitive regular expression match:

$ pip install pyfaidx
$ faidx nr.fasta --regex "(?i)streptomyces"
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written by Matt Shirley Matt Shirley

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