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ORIGINAL RESEARCH Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization
BibTeX
@MISC{Spirollari_originalresearch,
author = {Junilda Spirollari and Jason T. L. Wang and Kaizhong Zhang and Vivian Bellofatto and Bruce A. Shapiro},
title = {ORIGINAL RESEARCH Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization},
year = {}
}
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Abstract
Abstract: Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results from these algorithms are promising, an observation is that single sequence-based methods have moderate accuracy and more information is needed to improve on RNA secondary structure prediction, such as covariance scores obtained from multiple sequence alignments. We present in this paper a new approach to predicting the consensus secondary structure of a set of aligned RNA sequences via pseudo-energy minimization. Our tool, called RSpredict, takes into account sequence covariation and employs effective heuristics for accuracy improvement. RSpredict accepts, as input data, a multiple sequence alignment in FASTA or ClustalW format and outputs the consensus secondary structure of the input sequences in both the Vienna style Dot Bracket format and the Connectivity Table format. Our method was compared with some widely used tools including KNetFold, Pfold and RNAalifold. A comprehensive test on different datasets including Rfam sequence alignments and a multiple sequence alignment obtained from our study on the Drosophila X chromosome reveals that RSpredict is competitive with the existing tools on the tested datasets. RSpredict is freely available online as a web server and also as a jar file for download at
Keyphrases
original research predicting consensus structure multiple sequence alignment rna alignment via pseudo-energy minimization consensus secondary structure input data used tool tested datasets new approach input sequence comprehensive test clustalw format single sequence-based method moderate accuracy single rna sequence connectivity table format available online jar file free energy parameter covariance score accuracy improvement aligned rna sequence web server free energy minimization problem different datasets effective heuristic secondary structure pseudo-energy minimization rna secondary structure prediction vienna style dot bracket format thermodynamic process drosophila chromosome reveals account sequence covariation rfam sequence alignment
