Paper Info
Title
Structural Alignment of RNA with Triple Helix Structure.
Abstract
Structural alignment is useful in identifying members of ncRNAs. Existing tools are all based on the secondary structures of the molecules. There is evidence showing that tertiary interactions (the interaction between a single-stranded nucleotide and a base-pair) in triple helix structures are critical in some functions of ncRNAs. In this article, we address the problem of structural alignment of RNAs with the triple helix. We provide a formal definition to capture a simplified model of a triple helix structure, then develop an algorithm of O(mn 3) time to align a query sequence (of length m) with known triple helix structure with a target sequence (of length n) with an unknown structure. The resulting algorithm is shown to be useful in identifying ncRNA members in a simulated genome.
Year
DOI
Venue
2012
10.1089/cmb.2010.0052
JOURNAL OF COMPUTATIONAL BIOLOGY
Keywords
Field
DocType
algorithms,non-coding RNA,structural alignment,triple helix
Genome,RNA,Structural alignment,Formal description,Triple helix,Bioinformatics,Non-coding RNA,Mathematics
Journal
Volume
Issue
ISSN
19.0
4
1066-5277
Citations 
PageRank 
References 
3
0.39
6
Authors
2
Name
Order
Citations
PageRank
Thomas K. F. Wong1899.80
Siu-ming Yiu2102692.90