[Bioperl-l] seq_inds method question for blast parsing...

[Jason Stajich]

Can you try it with the 'blast' parser rather than the psiblast parser and
report any problems.

On Sat, 19 Oct 2002, Sajeev Batra US-OPERON-Alameda wrote:

> Hi Bioperl users,
>
> I've been using SearchIO for both NCBI and WashU BLASTN parsing as follows:
>
> my $in     = Bio::SearchIO->new( -format => 'psiblast' );
> my $writer = MyBlastWriter->new();
> my $out    = Bio::SearchIO->new( -format => 'psiblast',
> 				 -writer => $writer );
> while ( my $result = $in->next_result() ) {
>     #printf STDERR "Report %d: $result\n", $in->report_count;
>     $out->write_result($result);
> }
>
>
> seq_inds method usage is here in my to_string subroutine:
> my @seq_inds_array = $hit->seq_inds('query','identical',1);
> my @test_inds_array = $hit->seq_inds('subject','identical',1)
>
> The identities reported back are the correct number when the alignment has
> no gaps in it. :-)
> However when the alignment has at least one gap in it (my example has two
> gaps).  The
> number of indenties reported back are incorrect.  Some of the identity
> positions reported back
> are also off.  Usually the number of identities reported back are greater
> than the actual number.
>
> I'm wondering if anyone else has noticed that or could it be that there is
> another technique
> to account for gaps in a blast alignment?
>
> Your feedback would be appreciated!
>
> Thanks,
> Sajeev.
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu