Re: Getting pairwise alignment scores for existing multiple alignment
"Fields, Christopher J" <[email protected]>
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
On Sep 30, 2014, at 1:20 AM, Alexey Morozov <[email protected]<mailto:[email protected]>> wrote: Dear colleagues, Is there a method in bioperl that will calculate pairwise alignment scores for any given pair of genes in MSA (according to a given matrix and gap opening/extension cost)? It seems that Bio::SimpleAlign methods only work with score if it has been described in MSA file and can only hold a general multiple sequence alignment score. -- Alexey Morozov, LIN SB RAS, bioinformatics group. Irkutsk, Russia. Bio::Align::PairwiseStatistics appears to deal with this, see if it fits your needs. You may need to extract the pairwise alignment of the two genes if they are in a multiple sequence alignment. chris _______________________________________________ Bioperl-l mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/bioperl-l