Short Regular Expressions from Finite Automata: Empirical Results
CIAA '09 Proceedings of the 14th International Conference on Implementation and Application of Automata
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Controlled non-uniform random generation of decomposable structures
Theoretical Computer Science
A random testing approach using pushdown automata
TAP'11 Proceedings of the 5th international conference on Tests and proofs
Flexible RNA design under structure and sequence constraints using formal languages
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Non-redundant random generation algorithms for weighted context-free grammars
Theoretical Computer Science
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Summary: 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 Contact: dev.GenRGenS@lri.fr