Dna Pairwise Alignment Using Matlab

Question

[HMZ Gheidan]

Hey everybody I'm trying to implement a Matlab code (though there is a built in function) to do simple alignment for two DNA sequences. if anyone have an Idea help needed.

Thanks a lot in advance

[Arun]

Help in what manner?

[HMZ Gheidan]

as simple as I announced it is just 2 DNA sequences alignment, Im trying to start a student version for such a thing !

[Ying W]

also, gapped or ungapped

[HMZ Gheidan]

gapped ... as I saw it does not make a big change in the algorithm cause we will use the scoring tables !

Answer 1

[Gmoney]

Have you considered looking at Smith-Waterman examples?

http://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm

Here's an example in python: http://narnia.cs.ttu.edu/drupal/node/104