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

[Roy Chaudhuri]

I think the method you are referring to is available in the Tm_estimate 
method of Bio::SeqFeature::Primer3. That is the old method that was used 
for Tm calculation in BioPerl before the more accurate thermodynamic 
calculation was implemented:
http://bioperl.org/pipermail/bioperl-l/2004-February/014905.html

Roy.

Samantha Thompson wrote:
> Hi,
> 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 :)
> 
> Sam
> 
> -----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 
> Bio::SeqFeature::Primer.
> 
> Roy.
> 
> --
> 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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> 
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