Title

Efficient alignment of RNA secondary structures using sparse dynamic programming

Authors

Authors

C. C. Zhong;S. J. Zhang

Comments

Authors: contact us about adding a copy of your work at STARS@ucf.edu

Abbreviated Journal Title

BMC Bioinformatics

Keywords

NONCODING RNAS; EDIT DISTANCE; TREE EDIT; PREDICTION; ELEMENTS; GENOME; TRANSCRIPTOME; SEQUENCES; MOTIFS; SPACE; Biochemical Research Methods; Biotechnology & Applied Microbiology; Mathematical & Computational Biology

Abstract

Background: Current advances of the next-generation sequencing technology have revealed a large number of un-annotated RNA transcripts. Comparative study of the RNA structurome is an important approach to assess their biological functionalities. Due to the large sizes and abundance of the RNA transcripts, an efficient and accurate RNA structure-structure alignment algorithm is in urgent need to facilitate the comparative study. Despite the importance of the RNA secondary structure alignment problem, there are no computational tools available that provide high computational efficiency and accuracy. In this case, designing and implementing such an efficient and accurate RNA secondary structure alignment algorithm is highly desirable. Results: In this work, through incorporating the sparse dynamic programming technique, we implemented an algorithm that has an O(n(3)) expected time complexity, where n is the average number of base pairs in the RNA structures. This complexity, which can be shown assuming the polymer-zeta property, is confirmed by our experiments. The resulting new RNA secondary structure alignment tool is called ERA. Benchmark results indicate that ERA can significantly speedup RNA structure-structure alignments compared to other state-of-the-art RNA alignment tools, while maintaining high alignment accuracy. Conclusions: Using the sparse dynamic programming technique, we are able to develop a new RNA secondary structure alignment tool that is both efficient and accurate. We anticipate that the new alignment algorithm ERA will significantly promote comparative RNA structure studies. The program, ERA, is freely available at http://genome.ucf.edu/ERA.

Journal Title

Bmc Bioinformatics

Volume

14

Publication Date

1-1-2013

Document Type

Article

Language

English

First Page

15

WOS Identifier

WOS:000324288000001

ISSN

1471-2105

Share

COinS