How to execute smith waterman algorithm in matlab?
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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?
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Walter Roberson
2015-10-16
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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.
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Vanessa Srebny
2019-4-29
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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
1 个评论
Walter Roberson
2019-4-30
? 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).
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