CENTROIDFOLD: a web server for RNA secondary structure prediction
Open Access
- 12 May 2009
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 37 (Web Server), W277-W280
- https://doi.org/10.1093/nar/gkp367
Abstract
The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the server predicts a common secondary structure. Usage of the server is quite simple. You can paste a single RNA sequence (FASTA or plain sequence text) or a multiple alignment (CLUSTAL-W format) into the textarea then click on the ‘execute CentroidFold’ button. The server quickly responses with a prediction result. The major advantage of this server is that it employs our original CentroidFold software as its prediction engine which scores the best accuracy in our benchmark results. Our web server is freely available with no login requirement.Keywords
This publication has 10 references indexed in Scilit:
- Prediction of RNA secondary structure using generalized centroid estimatorsBioinformatics, 2008
- Centroid estimation in discrete high-dimensional spaces with applications in biologyProceedings of the National Academy of Sciences, 2008
- CONTRAfold: RNA secondary structure prediction without physics-based modelsBioinformatics, 2006
- RNA secondary structure prediction by centroids in a Boltzmann weighted ensembleRNA, 2005
- Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure predictionBMC Bioinformatics, 2004
- A statistical sampling algorithm for RNA secondary structure predictionNucleic Acids Research, 2003
- Pfold: RNA secondary structure prediction using stochastic context-free grammarsNucleic Acids Research, 2003
- Vienna RNA secondary structure serverNucleic Acids Research, 2003
- The equilibrium partition function and base pair binding probabilities for RNA secondary structureBiopolymers, 1990
- Optimal computer folding of large RNA sequences using thermodynamics and auxiliary informationNucleic Acids Research, 1981