[Bioperl-l] Will subseq give complement?

[Gray, John]

I am trying to write a script which pull only intron sequences from genomic contigs, and I am having trouble making subseq give me the complement of the sequence in the file.  First I import the file into the bioperl object $seq using SeqIO, and then I process the features.  When the feature is an 'mRNA', with a 'SplitLocation', then I put all the exon stop and start positions into @start and @end arrays.  I then pull the intron sequence with the following command:

                    $sequence = $seq->subseq($end[$j]+1,$start[$j+1]-1, ' ', $strand);

This whole process works great, except that I always only get the top strand, regardless of the orientation of the feature.  I have confirmed that in fact the $strand variable properly reflects the strand of the feature.

Am I using this method properly?  Can anyone help me?



John T. Gray, Ph.D.
Director, Vector Development & Production
Experimental Hematology Division
Hematology-Oncology
St. Jude Children's Research Hospital
 
(901) 495-4729 phone
(901) 495-2176 fax
John.Gray at stjude.org