Bioperl: SeqAlign BLAST parsing

[Joe Ryan]

Andreas,

One problem with relying on the ASN.1 outputs is you can only get 
ASN.1 outputs when BLASTing against GENBANK datasets.  (this is 
because of the format of the deflines >db|gi|accession ).

You may want to take a look at one of the existing BLAST parsers...

Bio::Tools::Blast
http://bio.perl.org/

Ian Korf's BP2.pm
http://sapiens.wustl.edu/~ikorf/bioinformatics.html

NHGRI::Blastall
http://genome.nhgri.nih.gov/blastall/

joe
--
Joseph Ryan
Programmer
National Human Genome Research Institute


On Wed, Oct 27, 1999 at 03:35:03PM -0400, Andreas Matern wrote:
> With a local installation of the NCBI toolbox, one has the option of
> creating SeqAlign output for blast results.  Although obviously not meant to
> be human readable, the output does have the benefit of being more easily
> parsed than the conventional BLAST output.  Are any groups out there using
> the SeqAlign option of blastall?  Just wondering if I'm going down a
> dead-end road that someone else has already traveled.
> 
> Sincerely,
> 
> Andreas
> 
> ---------------
> Andreas Matern
> 622 Rhodes Hall
> Cornell Theory Center
> Ithaca, NY 14853
> 
> alm13@cornell.edu
> http://syntom.cit.cornell.edu/
> 
> 
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