[Bioperl-l] BLASTing with a seqio/seq object...

Chris Fields cjfields at uiuc.edu
Thu Nov 30 12:12:32 EST 2006


> Hi,
> Thanks for helping me with the BLAST code, when I made the 
> corections in ran fine, I'm assuming the returned object 
> $blast_result is a kind of searchio object, although I'm not 
> sure. I tried the code on the bioperl tutorial page for 
> processing a searchio object returned from blast....
> http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA
> STA_reports_with_Search_and_SearchIO
> this seems to be the next stage after blasting in the bioperl 
> tutorial but I'm sure how to process it correctly to get hit 
> and alignment information regards,
> 
> Samantha Thompson

It is a SearchIO object.  FYI, you also have the option of saving the raw
BLAST output to a file if needed (it should be described in the RemoteBlast
POD).

There is also a great HOWTO which goes into more detail about hits/HSPs and
how to get alignments:

http://www.bioperl.org/wiki/HOWTO:SearchIO


chris



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