[Bioperl-l] Getting pairwise alignment scores for existing multiple alignment

[Fields, Christopher J]

On Sep 30, 2014, at 1:20 AM, Alexey Morozov <alexeymorozov1991 at gmail.com<mailto:alexeymorozov1991 at gmail.com>> 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

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