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

Samantha Thompson Samantha.Thompson at greenbiologics.com
Mon Dec 8 10:35:42 EST 2008

Thanks for this.
However, I think it's common for molecular biologists I work with in the
lab to use primer calculation formulae that are different/simpler than
those often recommended by things like Primer3 and sigma's ordering
website. Typically, we use a formula from Maniartis et al (I think a
different author in later editions), Molecular Cloning. So I thought I'd
work up a calculator based on this.
I'll also take a look at the SeqStats module thanks for your help :)


-----Original Message-----
From: Roy Chaudhuri [mailto:rrc22 at cam.ac.uk] 
Sent: 08 December 2008 14:56
To: Samantha Thompson
Cc: bioperl-l List
Subject: Re: [Bioperl-l] Processing seq in Bio::Seq objects

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
> 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
> 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
> a bit of a mini local/proprietry strain and sequence database which
> 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
> 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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