Path: news.mathworks.com!not-for-mail
From: <HIDDEN>
Newsgroups: comp.soft-sys.matlab
Subject: Re: Bioinformatics Toolbox
Date: Mon, 16 Nov 2009 01:44:01 +0000 (UTC)
Organization: The MathWorks Inc
Lines: 8
Message-ID: <hdqap1$li0$1@fred.mathworks.com>
References: <hd1b1a$kj4$1@fred.mathworks.com> <394271442.11820.1258252508996.JavaMail.root@gallium.mathforum.org>
Reply-To: <HIDDEN>
NNTP-Posting-Host: webapp-05-blr.mathworks.com
Content-Type: text/plain; charset="ISO-8859-1"
Content-Transfer-Encoding: 8bit
X-Trace: fred.mathworks.com 1258335841 22080 172.30.248.35 (16 Nov 2009 01:44:01 GMT)
X-Complaints-To: news@mathworks.com
NNTP-Posting-Date: Mon, 16 Nov 2009 01:44:01 +0000 (UTC)
X-Newsreader: MATLAB Central Newsreader 222043
Xref: news.mathworks.com comp.soft-sys.matlab:585303


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?