How to execute smith waterman algorithm in matlab?

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suganya paramasivam
suganya paramasivam 2015-10-16
评论： Walter Roberson 2019-4-30
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
Walter Roberson 2015-10-16
  1 个评论
suganya paramasivam
suganya paramasivam 2015-10-16
Thank you so much for your quick response... I am sure this will be helpful for me to continue my project work..

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Vanessa Srebny
Vanessa Srebny 2019-4-29
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
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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