RNAalifold: improved consensus structure prediction for RNA alignments
Top Cited Papers
Open Access
- 11 November 2008
- journal article
- research article
- Published by Springer Nature in BMC Bioinformatics
- Vol. 9 (1), 474
- https://doi.org/10.1186/1471-2105-9-474
Abstract
The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach.Keywords
This publication has 42 references indexed in Scilit:
- Unifying evolutionary and thermodynamic information for RNA folding of multiple alignmentsNucleic Acids Research, 2008
- RNA STRAND: The RNA Secondary Structure and Statistical Analysis DatabaseBMC Bioinformatics, 2008
- Dinucleotide controlled null models for comparative RNA gene predictionBMC Bioinformatics, 2008
- ConStruct: Improved construction of RNA consensus structuresBMC Bioinformatics, 2008
- Centroid estimation in discrete high-dimensional spaces with applications in biologyProceedings of the National Academy of Sciences, 2008
- Strategies for measuring evolutionary conservation of RNA secondary structuresBMC Bioinformatics, 2008
- RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA moleculesBMC Bioinformatics, 2007
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectNature, 2007
- Efficient pairwise RNA structure prediction using probabilistic alignment constraints in DynalignBMC Bioinformatics, 2007
- Multiple sequence alignment with the Clustal series of programsNucleic Acids Research, 2003