# DNA sequence alignment

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.

Regards,
Rayne

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?

Thanks.

Hi,
Please any body provide me with a program which compute distance matrix from dna or protein sequences

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.

Regards,
Rayne
http://en.wikipedia.org/wiki/Smith-Waterman_algorithm#Example

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.
http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm

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.