Literature DB >> 15215368

ILM: a web server for predicting RNA secondary structures with pseudoknots.

Jianhua Ruan1, Gary D Stormo, Weixiong Zhang.   

Abstract

The ILM web server provides a web interface to two algorithms, iterated loop matching and maximum weighted matching, for efficiently predicting RNA secondary structures with pseudoknots. The algorithms can utilize either thermodynamic or comparative information or both, and thus can work on both aligned and individual sequences. Predicted secondary structures are presented in several formats compatible with a variety of existing visualization tools. The service can be accessed at http://cic.cs.wustl.edu/RNA/.

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Year:  2004        PMID： 15215368      PMCID： PMC441582          DOI： 10.1093/nar/gkh444

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  23 in total

1.  RNA secondary structure prediction based on free energy and phylogenetic analysis.

Authors:  V Juan; C Wilson
Journal:  J Mol Biol       Date:  1999-06-18       Impact factor: 5.469

2.  An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.

Authors:  Jianhua Ruan; Gary D Stormo; Weixiong Zhang
Journal:  Bioinformatics       Date:  2004-01-01       Impact factor: 6.937

3.  GPRM: A genetic programming approach to finding common RNA secondary structure elements.

Authors:  Yuh-Jyh Hu
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 4.  Structural and functional aspects of RNA pseudoknots.

Authors:  E Dam; K Pleij; D Draper
Journal:  Biochemistry       Date:  1992-12-01       Impact factor: 3.162

5.  Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods.

Authors:  R R Gutell; A Power; G Z Hertz; E J Putz; G D Stormo
Journal:  Nucleic Acids Res       Date:  1992-11-11       Impact factor: 16.971

6.  Inferring consensus structure from nucleic acid sequences.

Authors:  D K Chiu; T Kolodziejczak
Journal:  Comput Appl Biosci       Date:  1991-07

7.  An RNA folding method capable of identifying pseudoknots and base triples.

Authors:  J E Tabaska; R B Cary; H N Gabow; G D Stormo
Journal:  Bioinformatics       Date:  1998       Impact factor: 6.937

8.  A dynamic programming algorithm for RNA structure prediction including pseudoknots.

Authors:  E Rivas; S R Eddy
Journal:  J Mol Biol       Date:  1999-02-05       Impact factor: 5.469

9.  Using multiple alignments and phylogenetic trees to detect RNA secondary structure.

Authors:  B Gulko; D Haussler
Journal:  Pac Symp Biocomput       Date:  1996

10.  Graph-theoretic approach to RNA modeling using comparative data.

Authors:  R B Cary; G D Stormo
Journal:  Proc Int Conf Intell Syst Mol Biol       Date:  1995
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  11 in total

1.  RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

Authors:  Marie-Josée Cros; Antoine de Monte; Jérôme Mariette; Philippe Bardou; Benjamin Grenier-Boley; Daniel Gautheret; Hélène Touzet; Christine Gaspin
Journal:  RNA       Date:  2011-09-23       Impact factor: 4.942

2.  The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting.

Authors:  Durga M Chadalavada; Elizabeth A Gratton; Philip C Bevilacqua
Journal:  Biochemistry       Date:  2010-06-29       Impact factor: 3.162

3.  RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers.

Authors:  Eckart Bindewald; Bruce A Shapiro
Journal:  RNA       Date:  2006-03       Impact factor: 4.942

4.  A distinct group of hepacivirus/pestivirus-like internal ribosomal entry sites in members of diverse picornavirus genera: evidence for modular exchange of functional noncoding RNA elements by recombination.

Authors:  Christopher U T Hellen; Sylvain de Breyne
Journal:  J Virol       Date:  2007-03-28       Impact factor: 5.103

Review 5.  Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships.

Authors:  Susan J Schroeder
Journal:  J Virol       Date:  2009-04-15       Impact factor: 5.103

6.  Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis.

Authors:  Andrea L Cerrone-Szakal; Durga M Chadalavada; Barbara L Golden; Philip C Bevilacqua
Journal:  RNA       Date:  2008-07-24       Impact factor: 4.942

Review 7.  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

8.  Fine-tuning structural RNA alignments in the twilight zone.

Authors:  Andreas Bremges; Stefanie Schirmer; Robert Giegerich
Journal:  BMC Bioinformatics       Date:  2010-04-30       Impact factor: 3.169

9.  RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology.

Authors:  Michela Taufer; Ming-Ying Leung; Thamar Solorio; Abel Licon; David Mireles; Roberto Araiza; Kyle L Johnson
Journal:  Parallel Comput       Date:  2008-11-01       Impact factor: 0.986

10.  Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.

Authors:  Samuel Bleckley; Jonathan W Stone; Susan J Schroeder
Journal:  PLoS One       Date:  2012-12-27       Impact factor: 3.240
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