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

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Thu Jul 14 06:53:17 EDT 2005


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

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',
=> $hit->raw_score,
=> $hit->name,
=> {
                                                            locus_tag =>
note      => $note,

# @hsps is a filtered list of HSPs obtained from $hit->next_hsp
foreach $hsp (@hsps) {

$genome->add_SeqFeature($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

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