MATLAB Central Newsreader - Bioinformatics Toolbox

Bioinformatics Toolbox

Fri, 06 Nov 2009 01:38:02 -0500

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

Re: Bioinformatics Toolbox

Lucio Cetto — Fri, 06 Nov 2009 14:15:06 -0500

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)

Re: Bioinformatics Toolbox

Karen — Sun, 15 Nov 2009 02:34:38 -0500

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

Re: Bioinformatics Toolbox

Lucio Cetto — Mon, 16 Nov 2009 01:44:01 -0500

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?