[Bioperl-l] Blast features added to wrong strand???

[Jason Stajich]

Why use bl2seq when you can use fasta....

 From the Bio::SearchIO::blast documentation

=head2 bl2seq parsing

Since I cannot differentiate between BLASTX and TBLASTN since bl2seq
doesn't report the algorithm used - I assume it is BLASTX by default -
you can supply the program type with -report_type in the SearchIO
constructor i.e.

   my $parser = new Bio::SearchIO(-format => 'blast',
                                  -file => 'bl2seq.tblastn.report',
                                  -report_type => 'tblastn');

This only really affects where the frame and strand information are
put - they will always be on the $hsp-E<gt>query instead of on the
$hsp-E<gt>hit part of the feature pair for blastx and tblastn bl2seq
produced reports.  Hope that's clear...


On Jul 14, 2005, at 6:53 AM, michael watson ((IAH-C)) wrote:

> Hi
>
> I'm using bioperl-1.4.
>
> I have a genomic region.  I am first using bl2seq and blastn to  
> align it
> with some custom sequences, then blastall and blastx to blast it  
> agains
> uniprot.
>
> I'm using SearchIO and pretty standard code to add the blast hits as
> features to the sequence e.g.:
>
> my $feature = Bio::SeqFeature::Generic->new(-primary_tag  => 'CDS',
>                               -score
> => $hit->raw_score,
>                               -display_name
> => $hit->name,
>                                -tag
> => {
>                                                              
> locus_tag =>
> $name,
>
> note      => $note,
>                                                               }
>                                 );
>
> # @hsps is a filtered list of HSPs obtained from $hit->next_hsp
> foreach $hsp (@hsps) {
>     $feature->add_sub_SeqFeature($hsp,'EXPAND');
> }
>
> $genome->add_SeqFeature($feature); # $genome is a Bio::Seq feature
>
> Now, the bl2seq hits all have the strand reported as "Plus / Minus"  
> and
> the blastx hits all have the strand reported as -1 i.e. there is a  
> gene
> on the other strand of my sequence.
>
> HOWEVER, using the above code for both the bl2seq results and the  
> blastx
> results, ONLY the blastx results get annotated on the reverse strand -
> the bl2seq results, which report the strand as "Plus / Minus", get
> annotated on the forward strand and hence point the wrong way when I
> draw them :-(
>
> So my question is, what am I doing wrong in the above code (which is
> pretty much ripped off from the bioperl HOWTOs) that makes the bl2seq
> "Plus / Minus" hits get annotated on the plus strand on my sequence??
>
> Many thanks
> Mick
>
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>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/