Multiple alignment tools

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vl80
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Multiple alignment tools

Post by 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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GaryGaulin
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Post by 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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JackBean
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Post by JackBean » Sun Nov 04, 2012 10:11 am

Why do you need to reformat it? Why do you want to use AC?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

jungleman67
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Post by 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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Post by leesajohnson » Tue Sep 13, 2016 8:46 am

Sequence alignment is a fantastically powerful analytical tool in many sciences needing pattern recognition work. Sequence alignment is a subfield of stringology. The term stringology is a popular nickname for string algorithms. Usually, text and string have the same meaning and they are the basic types to carry information. Thus the improvement of stringology will benefit many other fields. Subfields of stringology include string matching, pattern matching, periodicities, data structure, text compression and sequence alignment. https://www.amazon.com/Time-Warps-Strin ... 1575862174
https://www.expasy.org/genomics/sequence_alignment
https://en.wikipedia.org/wiki/List_of_s ... t_software

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