wise -- comparison of biopolymers, commonly DNA and protein sequence (fwd)
Hi,
I just want to proxy the Mail of Philipp Benner who just builded the
wise packages. I have just done a sponsored upload and I expect the
packages soon to hit the mirrors.
Kind regards and thanks to Philipp
Andreas.
Package: wise
Severity: wishlist
Wise2 is a package focused on comparisons of biopolymers, commonly DNA
sequence and protein sequence. There are many other packages which do
this, probably the best known being BLAST package (from NCBI) and the
Fasta package (from Bill Pearson). There are other packages, such as
the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
on hidden Markov models (HMMs) of biopolymers.
Wise2's particular forte is the comparison of DNA sequence at the level
of its protein translation. This comparison allows the simultaneous
prediction of say gene structure with homology based alignment. There is
currently no other package that I know of that contains this type of
algorithm with a full blown gene prediction model and a hidden Markov
model of a protein domain.
Wise2 also contains other algorithms, such as the venerable Smith-Waterman
algorithm, or more modern ones such as Stephen Altschul's generalised
gap penalties, or even experimental ones developed in house, such as
dba (see section \ref{sec:dba}). The development of these algorithms
is due to the ease of developing such algorithms in the enviroment
used by Wise2.
Wise2 has also been written with an eye for reuse and maintainability.
Although it is a pure C package you can access its functionality
directly in Perl. Parts of the package (or the entire package) can
be used by other C or C++ programs without namespace clashes as all
externally linked variables have the unqiue identifier Wise2 prepended.
Java and CORBA ports are being considered - see \ref{sec:api} the
API section
Finally Wise2, although implemented in C makes heavy use of the Dynamite
code generating language. Dynamite was written for this project, by
Ewan Birney. There is a separate documentation for Dynamite found at
http://www.sanger.ac.uk/Software/Dynamite.
Downloaded from:
ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
License: GPL
License for dynlibsrc:
All of the documentation and software included in the dynlibsrc
directory of the Wise2 package directory is copyrighted by Genome
Research Limited (GRL) and other individuals where appropriate. This
license is modelled after the 'BSD' style license and is appropriate
for use by both academic and commericial sites, without placing any
restriction on the distribution of source code from other sources with
this software.
Copyright 1998, 1999, GRL and others.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
1.Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2.Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the
distribution.
3.Neither the name GRL nor the names of its contributors may be used
to endorse or promote products derived from this software without
specific prior written permission.
It is considered polite to indicate where appropriate that software which
is developed using this source code includes a statement that it was developed
using the Wise2 soure code. This is not a requirement however.
THIS SOFTWARE IS PROVIDED BY THE GRL AND CONTRIBUTORS ``AS IS'' AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE GRL OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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