[Bioperl-l] Clustalw alignment parsing

[Fields, Christopher J]

On Sep 27, 2012, at 10:09 PM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> 2012/9/27 Antonio Nhani Jr <antonio.nhanijr at gmail.com>
> 
>> 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
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>> 
> 
> 
> 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

Have a look at Bio::Tools::Primer3Redux (on CPAN) for a BioPerl-based wrapper around Primer3.  

https://metacpan.org/release/Bio-Tools-Primer3Redux

chris