[Bioperl-l] getting strand from Bio::Align::AlignI ??

Jason Stajich jason at bioperl.org
Mon Mar 15 13:11:27 EDT 2010

Did you start with  Bio::SearchIO object and call get_aln on the HSP 
object?  Strand is available from the $hsp->query->strand and 
$hsp->hit->strand and Bio::SearchIO is the preferred way of parsing 
pairwise alignment reports.

Either way the sequences themselves have strands not the alignment.

Each sequence should have a strand $seq->strand since they are 
Bio::LocatableSeq objects.

for my $seq ( $aln->each_seq ) {
  print $seq->id, " ", $seq->strand, "\n";

Joan Pontius wrote, On 3/15/10 8:49 AM:
> I am looking into using Bio::Align::AlignI for an application that 
> uses blast2seq
> and can't figure out how to get the strand of an alignment?
> Thanks in advance
> Joan Pontius-Contractor SAIC
> Laboratory of Genomic Diversity
> Bldg 560-NCI
> Frederick Maryland 21702
> phone (301)846-1761
> fax (301) 846-1686 

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