glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity

Authors:
Prapaporn Techa-angkoon;Yanni Sun
Affiliations:
Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A.;Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A.
Venue:
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Year:
2013

Citing 4
Cited 0

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments

Bioinformatics
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements

Bioinformatics
The WEKA data mining software: an update

ACM SIGKDD Explorations Newsletter
Designing Filters for Fast-Known NcRNA Identification

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Quantified Score

Hi-index	0.00

Visualization

Abstract

Generating reliable alignments for ncRNAs is an important step in ncRNA secondary structure prediction and ncRNA gene finding. Existing sequence alignment programs can generate reliable alignments for ncRNAs with high sequence conservation. For highly structured ncRNAs that may lack strong sequence similarity, structural alignment programs are required. However, conducting reliable structural alignment is much more expensive than sequence alignment and is not ideal for large-scale input such as whole genomes or next-generation sequencing data. In this paper, we propose an accurate ncRNA alignment approach to align highly structured ncRNAs using only sequence similarity. By incorporating posterior probability and a machine learning approach, we can generate accurate alignments of highly structured ncRNAs without using structural information. We tested our approach on over three hundreds of pairs of highly structured ncRNAs from BRAliBase 2.1. The experimental results show that our approach can achieve more accurate alignments than commonly used sequence alignment programs and a popular structural alignment tool. The source codes of glu-RNA can be downloaded at http://sourceforge.net/projects/glu-rna/.