[Bioperl-l] Processing seq in Bio::Seq objects

Roy Chaudhuri roy.chaudhuri at gmail.com
Mon Dec 8 10:18:58 EST 2008

Hi Sam.

For nucleotide counts look at Bio::Tools::SeqStats. However, there is
already code for calculating primer melting temperatures in BioPerl, in


Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

Samantha Thompson wrote:
> Hi,
> I'm trying to find out if Bio::Seq or related has any built in routines
> for telling me things like how many of each of Gs Ts Cs and As (plus
> others) there are in a submitted DNA sequence. I'm writing a few little
> programs that do simple things like primer temperature calculation so
> something like GC content is good to know. Just thought I'd ask before
> writing the routines in Perl from scratch.
> Also, I'm implementing a lot of the web interface stuff to my bioperl
> (and other) routines using the Catalyst MVC framework modules in Perl.
> Just wondering what web frameworks any of you recommend if you're
> producing stuff that's available to others online. I'm currently making
> a bit of a mini local/proprietry strain and sequence database which I'm
> finding incorporating snippets of BioPerl more and more useful as I go
> along.
> Thanks,
> Sam
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina
> Sent: 07 December 2008 09:57
> To: Hilmar Lapp
> Cc: bioperl-l at lists.open-bio.org; Mark A. Jensen
> Subject: Re: [Bioperl-l] Problem in OMIM parser
> On Sat, Dec 6, 2008 at 20:28, Hilmar Lapp <hlapp at gmx.net> wrote:
>> On Dec 6, 2008, at 12:50 PM, Mark A. Jensen wrote:
>>  Dave- with developer response time like this, why doesn't everyone
> use
>>> Bioperl?-
>>> cheers-MAJ
>> You mean to imply that there are people who don't? ;)
> And ye shall know them by their code.   :)
> D
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