[Bioperl-l] Designing primers from multiple sequence alignment of amino acid sequences

[Bhakti Dwivedi]

Hi,

I have to design primers from the multiple sequence alignments of amino acid
sequences.  The sequences I am working with are quite diverged and often the
available primer design programs (such as CODEHOP/iCODEHOP) fail to find any
primer sets.   But, when I look  at the alignment manually, I could see the
regions that I could use to make primers.

So I  designed the degenerate primers the old-fashioned way, starting from
selecting the conserved regions (6-10aa long) from the alignment  to
translating the selected regions to DNA using the appropriate codon usage
table, and then finally checking the primer sets (potential forward and
reverse primers) using tools like OLIGOANALYZER.  In the end, I did find few
good primer sets, but getting them to work in reality is something I will
have to wait and see.

While doing this process manually, I really felt the need to automate it (it
was not just one alignment I did, I worked with several of those).   I was
wondering if there is anyway bioperl can help me here, or making a perl
script is the only way to go.

I would appreciate your suggestions/comments.  Thanks!  (apologize for a
long email..)


Regards
Bhakti