Thread Subject: Bioinformatics Toolbox

How to compute Fit Alignment using Matlab? (Semiglobal Alignment)

Look at the recently added function "localalign". If you have an old version of the toolbox by changing your sequences to profiles you can use profalign with the terminalgapadjust option set to false.
HTH
Lucio

"H " <harpreetj@gmail.com> wrote in message <hcvulq$bba$1@fred.mathworks.com>...
> How to compute Fit Alignment using Matlab? (Semiglobal Alignment)

Question about the 'localalign' function is this the same as the 'swalign' function found on MATLAB?

If you are doing an alignment without affine gaps and you only need the best local alignment, both functions should give you very similar results, if not equal.
Use LOCALALIGN if you need more than one local alignment between two sequences, and use SWALIGN if you need affine gaps.
HTH
Lucio

 
Karen <kwalker16@comcast.net> wrote in message <394271442.11820.1258252508996.JavaMail.root@gallium.mathforum.org>...
> Question about the 'localalign' function is this the same as the 'swalign' function found on MATLAB?