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Content
GenRGenS is a software dedicated to random generation of genomics sequences
that supports several classes of models :
- Markov chains: Homogenous, Framed, HMMs ...
- Context free grammars: Uniform, weighted
- Rational Languages: RegExps, PROSITE patterns
- Hierarchical models
You will find here the current
distribution of GenRGenS weither compressed (zip,tgz,rar) or not (tar), along
with some basic installation instructions.
A complete manual that contains tutorials for each class of random sequences
models is also available here.
It is also possible to browse and
download some typical description files to feed the software without having
to rewrite them from scratch.
GenRGenS Team
GenRGenS is being developped as a collaboration between Bioinformatics
group of LRI Orsay and group BIG
(Bioinformatique des Génomes) of IGM Orsay. Both are laboratories of
CNRS and Paris-Sud University.
- Developers :
- Current: Yann Ponty
- Previously : Frédéric Sarron, Loïc Boisseau and Olivier Ensch
- Biologist expert : Michel Termier.
- Project leader : Alain Denise.
Related publications
- Brief presentation of GenRGenS:
-
A. Denise, Y. Ponty and M. Termier.
Random Generation of structured genomic sequences
[pdf]
[bib]
Proceedings of RECOMB'03 (poster session), April 2003, Berlin.
- (In French) Yann Ponty. GenRGenS: génération aléatoire de séquences génomiques
[ps]. Poster presented at JOBIM 2002.
- Theoretical aspects of random generation of structures using weighted context-free
grammars:
- Alain Denise, Olivier Roques and Michel Termier. Random generation of words
of context-free languages according to the frequencies of letters
[ps].
In "Mathematics and Computer Science: Algorithms, Trees, Combinatorics and Probabilities".
Trends in Mathematics, Birkhaüser (2000) 113-125. Preliminary version.
- (In French) Alain Denise, Olivier Roques and Michel Termier. Génération aléatoire de séquences
génomiques structurées [ps], décembre 2001.
- A document which presents, more generally, algorithms for random generation
of structures, and models for random genomic sequences:
- (In French) Alain Denise. Structures aléatoires, modèles et analyse des génomes
[ps].
Mémoire d'Habilitation à Diriger les Recherches, décembre 2001.
Contact
- To suggest improvements for the next versions of GenRGenS:
- To report bugs:
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