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
GenRGenS: Software for generating random genomic sequences and structures
Bioinformatics, June 2006 22(12):1534-1535.
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).
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.)