On Sep 27, 2012, at 10:09 PM, Alexey Morozov
> 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
>> Haven't found a method in Bio::SimpleAlignIO to do this…
>> Any hint?
>> All the very best,
>> Bioperl-l mailing list
>> [email protected]
> Hi Antonio,
> Seems like there is no primer design module, Bio::SeqFeature::Primer
> only to annotate them and find melting temperatures. Is it truly
> 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.
Have a look at Bio::Tools::Primer3Redux (on CPAN) for a BioPerl-based
wrapper around Primer3.