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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