Local RNA base pairing probabilities in large sequences
Open Access
- 20 December 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 22 (5) , 614-615
- https://doi.org/10.1093/bioinformatics/btk014
Abstract
Summary: The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically unknown, arbitrary sequence windows have to be used in practice. Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window. Availability: The program RNAplfold is part of the Vienna RNA Package and can be downloaded from Author Webpage Contact:ivo@tbi.univie.ac.atKeywords
This publication has 9 references indexed in Scilit:
- Identification of clustered microRNAs using an ab initio prediction methodBMC Bioinformatics, 2005
- MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisonsBioinformatics, 2005
- Identification of microRNAs of the herpesvirus familyNature Methods, 2005
- Alignment of RNA base pairing probability matricesBioinformatics, 2004
- Prediction of locally stable RNA secondary structures for genome-wide surveysBioinformatics, 2004
- The microRNA RegistryNucleic Acids Research, 2004
- RNA folding at elementary step resolutionRNA, 2000
- Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology, 1999
- The equilibrium partition function and base pair binding probabilities for RNA secondary structureBiopolymers, 1990