Exact matching of RNA secondary structure patterns

Many RNA structures are assembled from a collection of RNA motifs, which appear repeatedly and in various combinations. Identification of RNA structural motifs will enhance our understanding of RNA structures and functions. Searching for secondary structural patterns in sequence databases is the bas...

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Bibliographic Details
Published inTheoretical computer science Vol. 335; no. 1; pp. 53 - 66
Main Authors Xu, Ying, Wang, Lusheng, Zhao, Hao, Li, Jianping
Format Journal Article
LanguageEnglish
Published Elsevier B.V 01.05.2005
Subjects
Algorithm
Match
RNA
RNA
Algorithm
Match
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Summary:Many RNA structures are assembled from a collection of RNA motifs, which appear repeatedly and in various combinations. Identification of RNA structural motifs will enhance our understanding of RNA structures and functions. Searching for secondary structural patterns in sequence databases is the basic technique and fundamental problem for extracting and identifying such motifs. A number of algorithms and programs have been developed for this purpose. In this paper, we adopt a representation of secondary structure called secondary expressions, and present two algorithms for finding all exact matches of a given secondary expression.
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ISSN:0304-3975
1879-2294
DOI:10.1016/j.tcs.2004.12.016