[Bioperl-l] Clustalw alignment parsing

Alexey Morozov alexeymorozov1991 at gmail.com
Thu Sep 27 23:09:49 EDT 2012

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.


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