[Bioperl-l] Clustalw alignment parsing
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,
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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.
More information about the Bioperl-l