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DNA sequence alignment

  1. Aug 4, 2007 #1
    Hi all,
    I'm interested in learning more about DNA sequence alignment and have been reading up on the topic online.

    I'm more interested in the Smith-Waterman algorithm for local alignment, but I'm quite confused about how the algorithm works.

    I know the algorithm works on a MxN matrix, where M and N are the lengths of the 2 DNA sequences, but I'm not sure how the entries of the matrix came about. Also, I keep coming across the substitution matrices PAM and BLOSUM, but I thought they're mostly used for amino acid sequences and their matrix entries are predetermined. So how do they fit into the Smith-Waterman algorithm where the DNA sequences are different in different comparisons?

    Thank you.

  2. jcsd
  3. Aug 4, 2007 #2


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  4. Aug 8, 2007 #3
    I have another question. Say we compare sequence A with sequence B, C and D using Smith-Waterman algorithm, and the maximum score for each of the 3 comparisons are 1, 2 and 3 respectively. Does that mean sequence A and C are the most similar and therefore the most useful for future research? If not, how do we determine which 2 sequences are the most similar?

  5. Dec 15, 2009 #4
    Please any body provide me with a program which compute distance matrix from dna or protein sequences
  6. Dec 15, 2009 #5
  7. Dec 15, 2009 #6

    Your best bet is to work through this example.

    If you're new to local alignment, I suggest you start with Needleman-Wunsch - it's simpler, and a precursor to Smith-Waterman.

    If you're still stuck, try asking specific questions again, and I'll try to help you out.

    As for substitution matrices - substitutions between A and G (purines) or C and T (pyrimidines) are penalized less than a purine to a pyrimidine (or vice versa) just like how substitutions between phenylalanine and tyrosine are penalized less (similar side chains!)

    The reason why you come across PAM/BLOSUM is because Smith-Waterman (and Needleman-Wunsch) can be used not only for nucleotide sequence alignment, but amino acid sequence alignment as well. All that being said, you really ought to ignore substitution matrices for now.
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