Welcome

This is the homepage of GenRGenS, a software dedicated to random generation of genomics sequences that supports several classes of models, including Markov chains, HMM, context-free grammars, PROSITE patterns and more.

GenRGenS is being developped as a collaboration between Bioinformatics group of LRI Orsay and group BIG (Bioinformatique des Génomes) of IGM Orsay by Alain Denise, Yann Ponty and Michel Termier.

Academic users are invited (pretty please?;)) to cite the following paper:

Y. Ponty, M. Termier and A. Denise [pdf] [bib]
GenRGenS: Software for generating random genomic sequences and structures
Bioinformatics, June 2006 22(12):1534-1535.

News

2012-11-04 Release of GenRGenS 2.1

GenRGens now ships in its 2.1 version. This new minor version mainly contains bug fixes, including an overzealous grammar clean-up (kudos to Alois Dreyfus for reporting the bug and contributing a patch). The BuildMarkov tool has also been extended to allow for pseudocounts (a la Laplace's rule of succession).

2010-09-06 GenRGenS companion paper published in TCS

The article describes the theoretical foundations and properties of weighted context-free grammars, and appeared in the September 2010 edition of the journal of Theoretical Computer Science.

2006-07-06 GenRGenS at Jobim'06

A short talk about GenRGenS features is given at the major french Bioinformatics conference [ppt slides].

2006-06-15 Bioinformatics article released

GenRGenS v2.0 official release announcement can now be found here.

2006-04-01 GenRGenS v2.0 manual published as a research report !

The manual can now be referred to as the research report no 1447 of the LRI (Orsay, France).

License

GenRGenS is a free software under GNU license. GenRGenS uses the JavaCUP software for the analysis of input files. Thus, some java_cup v 0.10k files are bundled with GenRGenS distributions. (You can find here the legal notice of JavaCUP.)