Detecting conserved RNA secondary structures in viral genomes: The RADAR approach

Mugdha Khaladkar, Jason Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Conserved regions, or motifs, present among RNA secondary structures serve as a useful indicator for predicting the functionality of the RNA molecules. Automated detection or discovery of these conserved regions is emerging as an important research topic in health and disease informatics. In this short paper we present a new approach for detecting conserved regions in RNA secondary structures by the use of constrained alignment and apply the approach to finding structural motifs in some viral genomes. Our experimental results show that the proposed approach is capable of efficiently detecting conserved regions in the viral genomes and is comparable to existing methods. We implement our constrained structure alignment algorithm into a web server, called RADAR. This web server is fully operational and accessible on the Internet at http://datalab.njit.edu/biodata/rna/RSmatch/server.htm.

Original languageEnglish (US)
Title of host publicationIntelligence and Security Informatics
Subtitle of host publicationBiosurveillance - Second NSF Workshop, BioSurveillance 2007, Proceedings
Pages222-227
Number of pages6
StatePublished - Dec 24 2007
Event2nd NSF BioSurveillance Workshop, BioSurveillance 2007 - New Brunswick, NJ, United States
Duration: May 22 2007May 22 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4506 LNCS

Other

Other2nd NSF BioSurveillance Workshop, BioSurveillance 2007
CountryUnited States
CityNew Brunswick, NJ
Period5/22/075/22/07

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Khaladkar, M., & Wang, J. (2007). Detecting conserved RNA secondary structures in viral genomes: The RADAR approach. In Intelligence and Security Informatics: Biosurveillance - Second NSF Workshop, BioSurveillance 2007, Proceedings (pp. 222-227). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4506 LNCS).