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

Samantha Thompson Samantha.Thompson at greenbiologics.com
Mon Dec 8 09:34:29 EST 2008


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



-----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
>> Bioperl?-
>> cheers-MAJ
> You mean to imply that there are people who don't? ;)

And ye shall know them by their code.   :)

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