- #1
wu_weidong
- 32
- 0
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'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