"Lars Thomsen" <lthomsen at interlynx.net> wrote:
>I am looking for the best alignment program money can buy...
>If you know any that are good...please send me a mail..
>it will be a great help.
>Lars Thomsen, MSc. PhD
>lthomsen at interlynx.net>>>
DIALIGN is a novel program for pairwise and multiple
alignment of nucleic acid and protein sequences. It is
an implementation of an algorithm described in
Morgenstern, B., Dress, A., and Werner, T. 1996.
Multiple DNA and protein sequence alignment based on
Proc. Natl. Acad. Sci. 93, 12098 - 12103.
The central idea of DIALIGN is to construct alignments
by using pairs of similar segments of the sequences to
be aligned (so called "diagonals").
No gap penalty is employed - gaps correspond to the parts
of the sequences not belonging to any of the "diagonals"
included into the alignment.
In various test examples, DIALIGN was able to find functional
sites and weak local similarities that could not be detected
by other alignment methods.
The program is very easy to use and online help is provided.
Executables for various UNIX platforms (including LINUX)
together with a user guide and a test example are available
P.S. We are planning to release an improved version of DIALIGN
in the near future. If you want to test this new version - or
if you are not able to install the current version on your
computer - you may mail me your sequences and I will do the
alignment for you.