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Gmane
From: Alexey Morozov <alexeymorozov1991 <at> gmail.com>
Subject: Re: Clustalw alignment parsing
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Friday 28th September 2012 03:09:49 UTC (over 4 years ago)
2012/9/27 Antonio Nhani Jr 

> Hi All,
>
> I need to parse a several seqs clustalw alignment file, searching for
> regions to design primers (preference for not degenerated).
> The amplified region must have base(s) differences, to identify each seq.
> Haven't found a method in Bio::SimpleAlignIO to do this…
>
> Any hint?
>
> All the very best,
>
> Antonio
> _______________________________________________
> Bioperl-l mailing list
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


Hi Antonio,
Seems like there is no primer design module, Bio::SeqFeature::Primer allows
only to annotate them and find melting temperatures. Is it truly necessary
to find primers via pure bioperl? I mean, there are lots of primer design
tools out there, and if it's part of longer pipeline you can just write a
parser for their output.

Alexey
 
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