Downloading from nr data base.

Question

[Carlos Caicedo]

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

Answer 1

[Jake Warner]

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...

Answer 2

[Matt Shirley]

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"