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Multiple alignment tools

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Multiple alignment tools

Postby vl80 » Thu Oct 25, 2012 9:20 pm

I need to align about 500 sequences that range from 10000 to 30000 bp in length with an average lenght of about 20000. The only way I know to do it is to download FASTA, reformat in notepad or word then use CLUSTALW. However, this would be a very lenghtly procedure .
Are there any online free (preferably) or other alignment tools that would do the job with accession numbers ony?
Any advise is much appreciated.
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Postby GaryGaulin » Fri Oct 26, 2012 2:49 am

I did not try it yet, but UCSC Genome Bioinformatics has a "Custom Tracks" feature that would seem to be able to align what you need, by accession number:

http://genome-preview.ucsc.edu/cgi-bin/ ... id=2650221

Does that work for you?
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Postby JackBean » Sun Nov 04, 2012 10:11 am

Why do you need to reformat it? Why do you want to use AC?

Cis or trans? That's what matters.
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Postby jungleman67 » Tue Oct 29, 2013 1:42 am

Saeed Fahad made P Pyro Align which was made for that I think: http://www.ncbi.nlm.nih.gov/pubmed/23125479
Don't know where to find it though. And not sure about the length either.
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