Skip Navigation



Bioinformatics Advance Access published online on March 30, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl113
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/12/1534    most recent
btl113v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Ponty, Y.
Right arrow Articles by Denise, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ponty, Y.
Right arrow Articles by Denise, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received February 21, 2006
Revised March 13, 2006
Accepted March 21, 2006

Applications note

GenRGenS: software for generating random genomic sequences and structures

Yann Ponty 1, Michel Termier 2, and Alain Denise 1 *

1 LRI, UMR CNRS 8623, Université Paris-Sud 11, F91405 Orsay cedex, France
2 IGM, UMR CNRS 8621, Université Paris-Sud 11, F91405 Orsay cedex, France

* To whom correspondence should be addressed.
Alain Denise, E-mail: dev.GenRGenS{at}lri.fr


  Abstract

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 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.

Associate Editor: Martin Bishop
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
W. Shu, X. Bo, Z. Zheng, and S. Wang
RSRE: RNA structural robustness evaluator
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W314 - W319.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.