Pairwise alignment from a consensus in query

[Antony03]

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

[Brian Bushnell]

Are you interested in protein or nucleotide alignments?

[Antony03]

Ideally, I would like to try both.

[Brian Bushnell]

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.

[Antony03]

Thank you the answer. But, how can I make a local alignment with the resulting consensus? Is fasta36 or blast can handle it?

[Brian Bushnell]

Blast should be able to, if the consensus is good enough.

[kmcarr]

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.