[BioRuby] Blast with file as a query option?
kenglish at gmail.com
Mon Apr 6 00:13:37 UTC 2009
I have to very large local fasta files that wish to blast against one
another and parse the results in bio ruby. I'm wondering if there is a way
to mimic the behavior of this blast command:
blastall -p blastn -i Large_list_sequences_1.fasta -d Large_list_sequences_2
where Large_list_sequences_2 is a formatted fasta db. My current
implementation opens Large_list_sequences_1.fasta and goes through it
sequence by sequence. It seems to run pretty slow. I'm wondering if I can in
some way do the above blast command and loop through the results and get a
For any curious, my code is on github:
The file that is doing the blasts is under app/model/biodatabase.rb.
I'm trying to write a rails app uses biosql db and allows this biologist to
organize his sequences. I'm very new to bioinformatics but have a lot
experience with Ruby on Rails.
Thanks in advance for you help.
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