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<div>On Sep 30, 2014, at 1:20 AM, Alexey Morozov <<a href="mailto:alexeymorozov1991@gmail.com">alexeymorozov1991@gmail.com</a>> wrote:</div>
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<div>Dear colleagues,<br>
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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.<br clear="all">
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<font face="arial,helvetica,sans-serif">Alexey Morozov,<br>
LIN SB RAS, bioinformatics group.<br>
Irkutsk, Russia.<br>
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<div>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.</div>
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<div>chris</div>
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