Structural alignment of RNA with complex pseudoknot structure

Thomas K.F. Wong, T. W. Lam, Wing Kin Sung, S. M. Yiu

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Citation (Scopus)

Abstract

The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this paper, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings
Pages403-414
Number of pages12
DOIs
Publication statusPublished - 2009
Externally publishedYes
Event9th International Workshop on Algorithms in Bioinformatics, WABI 2009 - Philadelphia, PA, United States
Duration: 12 Sept 200913 Sept 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5724 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference9th International Workshop on Algorithms in Bioinformatics, WABI 2009
Country/TerritoryUnited States
CityPhiladelphia, PA
Period12/09/0913/09/09

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