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

Kevin Brown Kevin.M.Brown at asu.edu
Wed Jan 27 15:23:57 EST 2010

Bioperl is just a collection of tools, not a full blown application.
Most of what you want can be done with the objects available from within
the toolkit, but the application (perl script) would still need to be
written to put the objects to use. You could use clustalw from within
perl to align the sequences (Bio::Tools::Run::Alignment::Clustalw), find
the conserved regions (Bio::SimpleAlign), reverse translate them
(Bio::Tools::CodonTable), then come up with an algorithm for primer
analysis and selction (or even use other apps like primer3
(Bio::Tools::Run::Primer3) from within perl).

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Bhakti Dwivedi
> Sent: Wednesday, January 27, 2010 12:42 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Designing primers from multiple sequence 
> alignment ofamino acid sequences
> 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
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