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  • Clustering sequences based on sequence similarity

    I have 8000 protein sequences that I want to cluster based on similarity (not identity) and select the longest representative sequence from each cluster. I checked several tools like HiFix, SiliX, ClusTR but could not find the optimal solution. I want to do clustering as like CD-Hit does to reduce dataset but based on sequence similarity rather that sequence identity.

  • #2
    Perhaps USEARCH or if you want something much more complicated, OrthoMCL..
    Last edited by rhinoceros; 07-09-2013, 02:58 AM.
    savetherhino.org

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    • #3
      So you want to group by functional similarity?
      You can do this based on physio-chemical properties of the amino acids. You translate each amino acid into 5 different metrics and then use Discriminant Analysis of Principle Components to cluster based on these properties.Described here:http://www.biomedcentral.com/1471-2148/12/68

      I can provide you with file formats/tips if needs be
      Last edited by JackieBadger; 07-09-2013, 03:55 AM.

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      • #4
        Thanks, it seems interesting and I planned to use it later as currently I am not focused on functional similarity!
        Originally posted by JackieBadger View Post
        So you want to group by functional similarity?
        You can do this based on physio-chemical properties of the amino acids. You translate each amino acid into 5 different metrics and then use Discriminant Analysis of Principle Components to cluster based on these properties.Described here:http://www.biomedcentral.com/1471-2148/12/68
        I can provide you with file formats/tips if needs be

        Comment


        • #5
          Thanks for the reply!

          Originally posted by rhinoceros View Post
          Perhaps USEARCH or if you want something much more complicated, OrthoMCL..

          Comment

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