[Bioperl-l] Problem Parsing BLAST output

Dave Messina David.Messina at sbc.su.se
Fri Aug 20 09:48:28 EDT 2010

Hi Ben,

I would not use the script you posted — I don't think it does what you want.

If you haven't already, you should take a look at the beginners' HOWTO


 the SearchIO HOWTO


and the example scripts included with BioPerl:


Incidentally, it's a lot of fiddly data processing to parse blast reports for many contigs against multiple databases and then go back and collate the results by query. I'm not sure exactly what you want to do once you've separated by query — if you provide some more information, we could suggest ways to best get you where you want to go.

I will mention, though, that BLAST has the ability to search multiple separate databases in one go and collate the results for you. So that's something to consider.


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