Bioperl: SeqAlign BLAST parsing

[Andreas Matern]

Joseph,

Actually, you can get seqalign output on a non-genbank formatted database,
the output is only slightly different:

from this genbank formatted database:

                local
                  str "TOVDE85TH" ,
                gi 4691223 } ,

to this non-genbank formatted database:

                local
                  str "TOVDE85TH" ,
                general {
                  db "BL_ORD_ID" ,
                  tag
                    id 11003 } } ,


where TOVDE85TH is the query sequence and gi # 4691223 is the subject in the
first example and
TOVDE85TH is the query sequence and the 11,003rd entry in the 'homemade'
database is the subject in the second example.

This works well for me, as we are using an Oracle database to store the
sequences anyway.

The reason ASN.1 output is so attractive is the obvious ease in parsing and
the hope that no matter what  BLAST version comes my way, the SeqAlign
output won't be too different.  I spend my days doing a lot of TBLASTX
analysis and most of the avaiable parsers don't work so well with that
input.

Sincerely,

Andreas





> -----Original Message-----
> From: owner-vsns-bcd-perl@lists.uni-bielefeld.de
> [mailto:owner-vsns-bcd-perl@lists.uni-bielefeld.de]On Behalf Of Joe Ryan
> Sent: Wednesday, October 27, 1999 4:38 PM
> To: vsns-bcd-perl@lists.uni-bielefeld.de
> Cc: Andreas Matern
> Subject: Re: Bioperl: SeqAlign BLAST parsing
>
>
> 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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