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Article #2398Re: Converting Clustal alignment to a single consensus
From: Vince Mulholland
Date: Tue, 26 Jan 2010 10:46
Date: Tue, 26 Jan 2010 10:46
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3876 bytes
Duncan, A deceptively simple question, but one that doesn't seem to have a simple answer. I tried doing it in several ways, but none of the tools I usually use gave the desired results. The only way I have been able to get anywhere was a bit convoluted and requires access to the commercial program SeqMan (part of the Lasergene package from DNAStar). Import unaligned DNA sequence files into SeqMan and assemble them into a contig. You can adjust the consensus calling by playing about with the options in the SeqMan parameters. You can also edit the consensus by hand. Then all you need to do is save the consensus to a text file. This is not precisely what you wanted, but it seems to be the best available. Regards, Vince Vincent Mulholland Molecular Biology Unit Manager - Diagnostics & Molecular Biology Section Science and Advice for Scottish Agriculture (SASA) Hi Folks, Does anyone know of software or a web page that will take a Clustal .aln file and simply spew out a single consensus sequence? I have an alignment of thirty 2000bp nucleotide sequences and ideally want to simply stick a single letter consensus sequence into an isothermal primer design program. At the moment we are generating the consensus sequence by hand but it's a pain to do! Thanks Duncan -- I love deadlines. I especially like the whooshing noise they make as they go flying by. Duncan Clark GeneSys Ltd.
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