Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
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 arrow Search for citing articles in:
ISI Web of Science (36)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Rivas, E.
Right arrow Articles by Eddy, S. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rivas, E.
Right arrow Articles by Eddy, S. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 16 no. 4 2000
Pages 334-340
© 2000 Oxford University Press

The language of RNA: a formal grammar that includes pseudoknots

Elena Rivas 1 and Sean R. Eddy 1,*

1 Department of Genetics, Washington University, St. Louis, MO 63110, USA

Received on August 4, 1999 ; revised on October 25, 1999 ; accepted on November 4, 1999

*To whom correspondence should be addressed.

Motivation: In a previous paper, we presented a polynomial time dynamic programming algorithm for predicting optimal RNA secondary structure including pseudoknots. However, a formal grammatical representation for RNA secondary structure with pseudoknots was still lacking.

Results: Here we show a one-to-one correspondence between that algorithm and a formal transformational grammar. This grammar class encompasses the context-free grammars and goes beyond to generate pseudoknotted structures. The pseudoknot grammar avoids the use of general context-sensitive rules by introducing a small number of auxiliary symbols used to reorder the strings generated by an otherwise context-free grammar. This formal representation of the residue correlations in RNA structure is important because it means we can build full probabilistic models of RNA secondary structure, including pseudoknots, and use them to optimally parse sequences in polynomial time.

Contact: eddy{at}genetics.wustl.edu


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
 BioinformaticsHome page
Y. Cai, B. Hartnett, C. Gustafsson, and J. Peccoud
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
Bioinformatics, October 15, 2007; 23(20): 2760 - 2767.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. L. Jacobs, A. T. Belew, R. Rakauskaite, and J. D. Dinman
Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae
Nucleic Acids Res., January 12, 2007; 35(1): 165 - 174.
[Abstract] [Full Text] [PDF]

Home page
 IEICE Trans Inf & SystHome page
S. SEKI and S. KOBAYASHI
A Grammatical Approach to the Alignment of Structure-Annotated Strings
IEICE Trans D: Information, December 1, 2005; E88-D(12): 2727 - 2737.
[Abstract] [PDF]

Home page
 Nucleic Acids ResHome page
J. S. Pedersen, I. M. Meyer, R. Forsberg, P. Simmonds, and J. Hein
A comparative method for finding and folding RNA secondary structures within protein-coding regions
Nucleic Acids Res., September 24, 2004; 32(16): 4925 - 4936.
[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.