Literature DB >> 10890394

Prediction of RNA base pairing probabilities on massively parallel computers.

M Fekete1, I L Hofacker, P F Stadler.   

Abstract

We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The program can be used to routinely fold RNA sequences of more than 10,000 nucleotides. Applications to complete viral genomes are discussed.

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Year:  2000        PMID： 10890394     DOI： 10.1089/10665270050081441

Source DB:  PubMed          Journal:  J Comput Biol        ISSN： 1066-5277            Impact factor:   1.479


  6 in total

1.  Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.

Authors:  David H Mathews
Journal:  RNA       Date:  2004-08       Impact factor: 4.942

2.  GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops.

Authors:  M Shel Swenson; Joshua Anderson; Andrew Ash; Prashant Gaurav; Zsuzsanna Sükösd; David A Bader; Stephen C Harvey; Christine E Heitsch
Journal:  BMC Res Notes       Date:  2012-07-02

3.  Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element.

Authors:  Patrick C Gilligan; Pooja Kumari; Shimin Lim; Albert Cheong; Alex Chang; Karuna Sampath
Journal:  Nucleic Acids Res       Date:  2010-12-10       Impact factor: 16.971

4.  Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars.

Authors:  Zsuzsanna Sükösd; Bjarne Knudsen; Morten Vaerum; Jørgen Kjems; Ebbe S Andersen
Journal:  BMC Bioinformatics       Date:  2011-04-18       Impact factor: 3.169

5.  ViennaRNA Package 2.0.

Authors:  Ronny Lorenz; Stephan H Bernhart; Christian Höner Zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F Stadler; Ivo L Hofacker
Journal:  Algorithms Mol Biol       Date:  2011-11-24       Impact factor: 1.405

6.  Selection of antisense oligonucleotides based on multiple predicted target mRNA structures.

Authors:  Xiaochen Bo; Shaoke Lou; Daochun Sun; Wenjie Shu; Jing Yang; Shengqi Wang
Journal:  BMC Bioinformatics       Date:  2006-03-09       Impact factor: 3.169
  6 in total

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