How to execute smith waterman algorithm in matlab?

I want to get an optimal sequence for given set of sequences. So, I am using Smith Water-man algorithm. How to execute that algorithm in Matlab?

Answer 1

[Walter Roberson]

http://www.mathworks.com/help/bioinfo/ref/swalign.html

See also http://www.mathworks.com/matlabcentral/fileexchange/45831-matlab-audio-analysis-library/content/library/smithWaterman.m if you want code for the algorithm itself.

[suganya paramasivam]

Thank you so much for your quick response... I am sure this will be helpful for me to continue my project work..

Answer 2

[Vanessa Srebny]

Hej,

thanks for the post, I was trying to use your function to split my fasta file, however it only returns a file fasta.txt.1 nothing more. It is a big file more than 200000 characters it should be more than 1 resulting file right? I would like to use the Smith -Waterman function to compare a whole genome sequence to a protein sequence. When without splitting there are to many characters for matlab.

I attached my to 2 sequences:

Thank you very much :)

Vanessa

[Walter Roberson]

? Which function were you using to split your fasta file?

When I use fastaread() to read each of your files, and use swalign() to align them, I am able to do that provided that I do not ask for the undocumented fourth output of swalign. I can also nwalign() them, which gives a different answer (with larger gaps).