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wise

comparison of biopolymers, commonly DNA and protein sequences

Variants:
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.

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 environment 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.

Homepage:
Package version:2.4.1-10
Architecture:amd64
Distribution:Debian
Filename:wise_2.4.1-10_amd64.deb

/usr/share/doc/wise/README


README for Wise2/Dynamite development


Wise2/Dynamite is written and maintained by Ewan Birney
<birney@ebi.ac.uk>.

The paper for Genewise is:

GeneWise and Genomewise. Birney E, Clamp M, Durbin R.
Genome Res. 2004 May;14(5):988-95.


The paper for Dynamite is:

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.
Birney E, Durbin R.  Proc I
more»

/usr/share/doc/wise/README.Debian

wise for Debian
--------------------------------------------------------------------------------

You may want to copy /usr/share/doc/wise-doc/examles/* (distributed by wise-doc)
to your home directory and set WISECONFIGDIR appropriately.

 -- Philipp Benner <pbenner@uni-osnabrueck.de>, Mon, 14 Jan 2008 18:36:28 +0100

/usr/share/man/man1/dba.1.gz

DBA(1)                                                        DBA(1)



NAME
       dba — characterising shared regulatory regions of genomic DNA

SYNOPSIS
       dba [options ... ]  { seq1 seq2 }

DESCRIPTION
       dba  -  standing  for  Dna  Block  Aligner, was developped by
       Niclas Jareborg, Richard Durbin and Ewan Birney  for  charac‐
       terising  shared regulatory regions of ge
more»

/usr/share/man/man1/dnal.1.gz

DNAL(1)                                                      DNAL(1)



NAME
       dnal — ...

SY
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/usr/share/man/man1/estwise.1.gz

ESTWISE(1)                                                ESTWISE(1)



NAME
       estwise — comp
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/usr/share/man/man1/estwisedb.1.gz

ESTWISEDB(1)                                            ESTWISEDB(1)



NAME
       estwisedb  — a
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/usr/share/man/man1/genewise.1.gz

GENEWISE(1)                                              GENEWISE(1)



NAME
       genewise — com
more»

/usr/share/man/man1/genewisedb.1.gz

GENEWISEDB(1)                                          GENEWISEDB(1)



NAME
       genewise  —  a
more»

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