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  • huda
    Junior Member
    • Aug 2012
    • 2

    similarity matrix of sequence alignment

    hi,
    I'm PhD student , I'm working in sequence alignment field.

    I do alignment , and got similarity matrix.
    My problem is I do not know how I can deal with diagonal of this matrix .

    is it must be 1? or is it must the original values of the comparison the element with itself.

    if I placed it as 1's which represent the fully matching , in this case the other cell will be larger than diagonal.

    I do not know how I have to deal with it, because the elements of diagonal will affect the clustering method later

    thanks in advance
  • balaji
    Junior Member
    • Feb 2011
    • 9

    #2
    if you have sequences and you want to cluster them, why dont you cluster them directly why there is a need to do alignment then generate similarity matrix and further do clustering in the end.

    Comment

    • huda
      Junior Member
      • Aug 2012
      • 2

      #3
      Originally posted by balaji View Post
      if you have sequences and you want to cluster them, why dont you cluster them directly why there is a need to do alignment then generate similarity matrix and further do clustering in the end.
      thank you , I have to do alignment the sequences , I need to know the similarity among sequences by alignment them.

      Anyway, I resolved the problem, because this problem since long time.

      Many thanks for advice

      Comment

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