Literature DB >> 9390227

RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search.

M Brown1, C Wilson.   

Abstract

A model based on intersections of stochastic context free grammars is presented to allow for the modeling of RNA pseudoknot structures. The model runs relatively fast, having the same order running time as stochastic context free grammar parsers. The model is shown to be able to perform database searches and find RNA sequences which resemble RNA pseudoknots which bind biotin. The problem domain of RNA biotin binders has significance in the support of the RNA world model of early life on earth.

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Year:  1996        PMID： 9390227

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN： 2335-6928


  8 in total

1.  A heuristic approach for detecting RNA H-type pseudoknots.

Authors:  Chun-Hsiang Huang; Chin Lung Lu; Hsien-Tai Chiu
Journal:  Bioinformatics       Date:  2005-06-30       Impact factor: 6.937

2.  KnotSeeker: heuristic pseudoknot detection in long RNA sequences.

Authors:  Jana Sperschneider; Amitava Datta
Journal:  RNA       Date:  2008-02-26       Impact factor: 4.942

3.  Fast and accurate search for non-coding RNA pseudoknot structures in genomes.

Authors:  Zhibin Huang; Yong Wu; Joseph Robertson; Liang Feng; Russell L Malmberg; Liming Cai
Journal:  Bioinformatics       Date:  2008-08-07       Impact factor: 6.937

Review 4.  Computational methods in noncoding RNA research.

Authors:  Ariane Machado-Lima; Hernando A del Portillo; Alan Mitchell Durham
Journal:  J Math Biol       Date:  2007-09-04       Impact factor: 2.259

5.  Efficient known ncRNA search including pseudoknots.

Authors:  Cheng Yuan; Yanni Sun
Journal:  BMC Bioinformatics       Date:  2013-01-21       Impact factor: 3.169

6.  DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.

Authors:  Jana Sperschneider; Amitava Datta
Journal:  Nucleic Acids Res       Date:  2010-01-31       Impact factor: 16.971

7.  Evolving stochastic context--free grammars for RNA secondary structure prediction.

Authors:  James Wj Anderson; Paula Tataru; Joe Staines; Jotun Hein; Rune Lyngsø
Journal:  BMC Bioinformatics       Date:  2012-05-04       Impact factor: 3.169

8.  Accelerated probabilistic inference of RNA structure evolution.

Authors:  Ian Holmes
Journal:  BMC Bioinformatics       Date:  2005-03-24       Impact factor: 3.169
  8 in total

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