Literature DB >> 2474658

Pattern analysis of RNA secondary structure similarity and consensus of minimal-energy folding.

D A Konings1, P Hogeweg.   

Abstract

We describe an automated procedure to search for consensus structures or substructures in a set of homologous or related RNA molecules. The procedure is based on the calculation of optimal and sub-optimal secondary structures using thermodynamic rules for base-pairing by energy-minimization. A linear representation of the secondary structures of the related RNAs is used so that they can be compared and classified using standard alignment and clusterings programs. We illustrate the method by means of two sets of homologous small RNAs, U2 and U3, and a set of alpha-globin mRNAs and show that biologically interesting consensus structures are obtained.

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Year:  1989        PMID： 2474658     DOI： 10.1016/0022-2836(89)90468-3

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


  15 in total

1.  Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures.

Authors:  Junji Kitagawa; Yasuhiro Futamura; Kenji Yamamoto
Journal:  Nucleic Acids Res       Date:  2003-04-01       Impact factor: 16.971

Review 2.  Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life.

Authors:  Nobuto Takeuchi; Paulien Hogeweg
Journal:  Phys Life Rev       Date:  2012-06-13       Impact factor: 11.025

3.  Prediction of RNA secondary structure, including pseudoknotting, by computer simulation.

Authors:  J P Abrahams; M van den Berg; E van Batenburg; C Pleij
Journal:  Nucleic Acids Res       Date:  1990-05-25       Impact factor: 16.971

4.  Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes.

Authors:  M A Huynen; P Hogeweg
Journal:  J Mol Evol       Date:  1994-07       Impact factor: 2.395

5.  RNA multi-structure landscapes. A study based on temperature dependent partition functions.

Authors:  S Bonhoeffer; J S McCaskill; P F Stadler; P Schuster
Journal:  Eur Biophys J       Date:  1993       Impact factor: 1.733

6.  Automatic detection of conserved RNA structure elements in complete RNA virus genomes.

Authors:  I L Hofacker; M Fekete; C Flamm; M A Huynen; S Rauscher; P E Stolorz; P F Stadler
Journal:  Nucleic Acids Res       Date:  1998-08-15       Impact factor: 16.971

7.  Exploring phenotype space through neutral evolution.

Authors:  M A Huynen
Journal:  J Mol Evol       Date:  1996-09       Impact factor: 2.395

8.  Molecular analysis of a U3 RNA gene locus in tomato: transcription signals, the coding region, expression in transgenic tobacco plants and tandemly repeated pseudogenes.

Authors:  T Kiss; F Solymosy
Journal:  Nucleic Acids Res       Date:  1990-04-25       Impact factor: 16.971

9.  Distinct RNA motifs are important for coactivation of steroid hormone receptors by steroid receptor RNA activator (SRA).

Authors:  Rainer B Lanz; Bahram Razani; Aaron D Goldberg; Bert W O'Malley
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-20       Impact factor: 11.205

10.  An image processing approach to computing distances between RNA secondary structures dot plots.

Authors:  Tor Ivry; Shahar Michal; Assaf Avihoo; Guillermo Sapiro; Danny Barash
Journal:  Algorithms Mol Biol       Date:  2009-02-09       Impact factor: 1.405
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