Literature DB >> 12079347

Secondary structure prediction for aligned RNA sequences.

Ivo L Hofacker1, Martin Fekete, Peter F Stadler.   

Abstract

Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation. (c) 2002 Elsevier Science Ltd.

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Year:  2002        PMID： 12079347     DOI： 10.1016/S0022-2836(02)00308-X

Source DB:  PubMed          Journal:  J Mol Biol        ISSN： 0022-2836            Impact factor:   5.469


  253 in total

1.  Pfold: RNA secondary structure prediction using stochastic context-free grammars.

Authors:  Bjarne Knudsen; Jotun Hein
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  Vienna RNA secondary structure server.

Authors:  Ivo L Hofacker
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

3.  Sequence diversity and functional conservation of the origin of replication in lactococcal prolate phages.

Authors:  Jasna Rakonjac; Lawrence J H Ward; Anja H Schiemann; Paul P Gardner; Mark W Lubbers; Paul W O'Toole
Journal:  Appl Environ Microbiol       Date:  2003-09       Impact factor: 4.792

4.  Gene expression analysis using single molecule detection.

Authors:  Kerstin Korn; Paola Gardellin; Bohao Liao; Mario Amacker; Asa Bergström; Henrik Björkman; Agnès Camacho; Sabine Dörhöfer; Klaus Dörre; Johanna Enström; Thomas Ericson; Tatiana Favez; Michael Gösch; Adrian Honegger; Sandra Jaccoud; Markus Lapczyna; Erik Litborn; Per Thyberg; Holger Winter; Rudolf Rigler
Journal:  Nucleic Acids Res       Date:  2003-08-15       Impact factor: 16.971

5.  Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean.

Authors:  Geneviève Girard; Andreas Roussis; Alexander P Gultyaev; Cornelis W A Pleij; Herman P Spaink
Journal:  Nucleic Acids Res       Date:  2003-09-01       Impact factor: 16.971

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

Authors:  Jianhua Ruan; Gary D Stormo; Weixiong Zhang
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

7.  MSARI: multiple sequence alignments for statistical detection of RNA secondary structure.

Authors:  Alex Coventry; Daniel J Kleitman; Bonnie Berger
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-10       Impact factor: 11.205

8.  BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences.

Authors:  Rob Knight; Amanda Birmingham; Michael Yarus
Journal:  RNA       Date:  2004-09       Impact factor: 4.942

Review 9.  Computational analysis of riboswitch-based regulation.

Authors:  Eric I Sun; Dmitry A Rodionov
Journal:  Biochim Biophys Acta       Date:  2014-02-28

10.  Genetic characterization of feline calicivirus strains associated with varying disease manifestations during an outbreak season in Missouri (1995-1996).

Authors:  Victor G Prikhodko; Carlos Sandoval-Jaime; Eugenio J Abente; Karin Bok; Gabriel I Parra; Igor B Rogozin; Eileen N Ostlund; Kim Y Green; Stanislav V Sosnovtsev
Journal:  Virus Genes       Date:  2013-11-12       Impact factor: 2.332
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