RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)

2012 ◽  
Vol 12 (2) ◽  
pp. 305-319 ◽  
Author(s):  
Martina Réblová ◽  
Kamila Réblová
Keyword(s):  
Secondary Structure ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Rna Secondary Structure ◽  
Bioinformatics Tool ◽  
Multiple Sequence

scholarly journals Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

2010 ◽  
Vol 38 (21) ◽  
pp. 7353-7363 ◽  
Author(s):  
M. R. Aniba ◽  
O. Poch ◽  
J. D. Thompson
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Multiple Sequence

scholarly journals Predicting Consensus Structures for RNA Alignments via Pseudo-Energy Minimization

2009 ◽  
Vol 3 ◽  
pp. BBI.S2578 ◽  
Author(s):  
Junilda Spirollari ◽  
Jason T.L. Wang ◽  
Kaizhong Zhang ◽  
Vivian Bellofatto ◽  
Yongkyu Park ◽  
...  
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Energy Minimization ◽  
Secondary Structure Prediction ◽  
Sequence Alignments ◽  
Rna Sequences ◽  
Multiple Sequence ◽  
Consensus Secondary Structure

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 http://datalab.njit.edu/biology/RSpredict .

Sign in / Sign up

Export Citation Format

Share Document