Balík: wise (2.2.0-3)

comparison of biopolymers, commonly DNA and protein sequences

Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. 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. 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 unique identifier Wise2 prepended. Java and CORBA ports are being considered - see 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.

Značky: Field: Biology, Implemented in: C, User Interface: Command Line, Role: Program, Scope: Utility