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Old 01-22-2015, 01:34 PM   #1
Dave_Carlson
Junior Member
 
Location: San Diego, CA

Join Date: Sep 2013
Posts: 3
Default Converting Blast+ output to Fasta sequence files

Hi All,

I have a bioinformatics problem that I'm hoping others have encountered (and solved) already.

I have a transcriptome that I have BLASTed against itself to look for putatively-paralogous genes. Right now the Blastn results are in tab-separated format, with several thousand rows of results. After filtering the results to remove unhelpful stuff (e.g., very, very short hsp's or sequences that hit to themselves), what I would like to be able to do is take each hit between two sequences, find the full sequences in the original transcriptome fasta file and output the two sequences into a new fasta file. Ideally, I would like to able to do this in a relatively automated manner, so that I get separate fasta files for each hit from my Blastn results.

Is anybody aware of a script or utility that could do something like that? My coding skills are not great, and I'm hoping that I don't have to spend a lot of time inventing (reinventing?) the wheel on this. Any help or suggestions would be appreciated! Thanks.
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