Thread: Smith-Waterman algorithm

  1. 11-18-2008 #1
    eangaga
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    Smith-Waterman algorithm

    Thank you guys. I really appreciate it.
    I have also been looking for how to implement this algorithm:The Smith-Waterman algorithm is a well-known algorithm for performing local sequence alignment; that is, for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.
    I want to search a FASTA format file in a data base. Any reference will be good. I know the biology, i just cant put it in c++!!
  2. 11-18-2008 #2
    CornedBee
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    Wikipedia is usually the first stop. It probably won't give you enough information to implement an algorithm this complex, but its references might be informative.
    All the buzzt!
    CornedBee

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  3. 11-18-2008 #3
    eangaga
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    Quote Originally Posted by CornedBee View Post
    Wikipedia is usually the first stop. It probably won't give you enough information to implement an algorithm this complex, but its references might be informative.
    Any one knows any good place I can learn about this code?
  4. 11-18-2008 #4
    Salem
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    By "good" you mean "with C++ code examples" right?
    If you dance barefoot on the broken glass of undefined behaviour, you've got to expect the occasional cut.
    If at first you don't succeed, try writing your phone number on the exam paper.
  5. 11-19-2008 #5
    eangaga
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    Quote Originally Posted by Salem View Post
    By "good" you mean "with C++ code examples" right?
    Exactly!!!!!!!!!!! Thats what I mean. Please advise!
  6. 11-20-2008 #6
    Salem
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    Did you add "source code" to your search terms?
    http://clusty.com/search?query=Smith...Mozilla-search
    If you dance barefoot on the broken glass of undefined behaviour, you've got to expect the occasional cut.
    If at first you don't succeed, try writing your phone number on the exam paper.
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