Multiple alignment tools

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    • #16960
      vl80
      Participant

      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.

    • #112780
      GaryGaulin
      Participant

      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?

    • #112859
      JackBean
      Participant

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

    • #114643
      jungleman67
      Participant

      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.

    • #116112
      leesajohnson
      Participant

      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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