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Old 07-25-2014, 03:26 PM   #1
Location: Canada, Quebec

Join Date: Apr 2012
Posts: 53
Default Pairwise alignment from a consensus in query

I want to look for a specific gene in a genome sequence. The gene sequence is degenerate and a colleague has suggested that I should make a multiple alignment of orthologous genes, make a consensus and look for the gene with this consensus sequence.

Do you know a software which may produce a pairwise alignment from a consensus as a query sequence ?
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