# DNA sequence alignment

1. Aug 4, 2007

### wu_weidong

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

2. Aug 4, 2007

### Monique

Staff Emeritus
3. Aug 8, 2007

### wu_weidong

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.

4. Dec 15, 2009

### sundus

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

5. Dec 15, 2009

### farful

http://www.megasoftware.net/

6. Dec 15, 2009

### farful

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