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Old 07-25-2014, 03:26 PM   #1
Antony03
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Default Pairwise alignment from a consensus in query

Hello,
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 ?
Thank
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Old 07-25-2014, 09:53 PM   #2
Brian Bushnell
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Are you interested in protein or nucleotide alignments?
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Old 07-26-2014, 04:07 AM   #3
Antony03
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Ideally, I would like to try both.

Last edited by Antony03; 07-26-2014 at 06:09 AM.
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Old 07-27-2014, 09:00 AM   #4
Brian Bushnell
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Mothur can make a consensus from multiple sequences, but I'm not sure this approach will work very well; it doesn't do a very good job with highly divergent sequences. Still, worth trying. There's also PBDagCon (from PacBio) that generates a consensus from multiple sequences, though it is aimed at PacBio's error profiles rather than degenerate genes.
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Old 07-27-2014, 09:05 AM   #5
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Thank you the answer. But, how can I make a local alignment with the resulting consensus? Is fasta36 or blast can handle it?
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Old 07-27-2014, 09:15 AM   #6
Brian Bushnell
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Blast should be able to, if the consensus is good enough.
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Old 07-27-2014, 08:35 PM   #7
kmcarr
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PSI-BLAST was designed for this task. Provided a multiple sequence alignment of homologous sequences it creates a Position Specific Scoring Matrix (PSSM) which it then uses when searching a database for other potential homologs. This method is more sensitive than using a single sequence, even a consensus, because it weights more heavily the portions of the sequence which are more highly conserved.
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