GenRGenS: Software for Generating Random Genomic Sequences and Structures

Yann Ponty 1, 2 Michel Termier 3 Alain Denise 1, 3, 4, *
* Corresponding author
1 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also allows the user to combine several of these different models at the same time. Availability: Source and executable files of GenRGenS (in Java) and the complete user's manual are freely available at http://www.lri.fr/bio/GenRGenS
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Yann Ponty, Michel Termier, Alain Denise. GenRGenS: Software for Generating Random Genomic Sequences and Structures. Bioinformatics, Oxford University Press (OUP), 2006, 22 (12), pp.1534--1535. ⟨10.1093/bioinformatics/btl113⟩. ⟨inria-00548871⟩

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