[Bioperl-l] Intron handling in Bio::SeqFeature

[Rohan Fernandes]

Hello
I am a newbie to both Bioperl and PERL. I am using Bioperl for primer
design for PCR. Presently I want to use Bioperl as a preprocessor in a
pipeline that will use Primer3 for the actual design of primers. I am
using both EMBL and Genbank formatted files.

This is the problem I am facing. I am interested only in the coding
sequences of genes for designing primers. This means that for each gene
feature I require information about all the exons that make it up. The
primers I design should complement only exon sequences and not any intron
sequence. I read a previous message regarding mRNAs and a similar problem.
It would seem that Bioperl does not support this at present. Am I right?
However I would like to have this functionality. Could you give me
suggestions on how I could go about adding this functionality myself?

Regards
Rohan