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Fast Structural Similarity Search of Noncoding RNAs Based on Matched Filtering of Stem Patterns

Yoon, Byung-Jun and Vaidyanathan, P. P. (2007) Fast Structural Similarity Search of Noncoding RNAs Based on Matched Filtering of Stem Patterns. In: Conference Record of the Forty-First Asilomar Conference on Signals, Systems and Computers. IEEE , Piscataway, NJ, pp. 44-48. ISBN 978-1-4244-2109-1. https://resolver.caltech.edu/CaltechAUTHORS:20100825-133532010

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Abstract

Many noncoding RNAs (ncRNAs) have characteristic secondary structures that give rise to complicated base correlations in their primary sequences. Therefore, when performing an RNA similarity search to find new members of a ncRNA family, we need a statistical model - such as the profile- csHMM or the covariance model (CM) - that can effectively describe the correlations between distant bases. However, these models are computationally expensive, making the resulting RNA search very slow. To overcome this problem, various prescreening methods have been proposed that first use a simpler model to scan the database and filter out the dissimilar regions. Only the remaining regions that bear some similarity are passed to a more complex model for closer inspection. It has been shown that the prescreening approach can make the search speed significantly faster at no (or a slight) loss of prediction accuracy. In this paper, we propose a novel prescreening method based on matched filtering of stem patterns. Unlike many existing methods, the proposed method can prescreen the database solely based on structural similarity. The proposed method can handle RNAs with arbitrary secondary structures, and it can be easily incorporated into various search methods that use different statistical models. Furthermore, the proposed approach has a low computational cost, yet very effective for prescreening, as will be demonstrated in the paper.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1109/ACSSC.2007.4487161DOIUNSPECIFIED
http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4487161PublisherUNSPECIFIED
ORCID:
AuthorORCID
Vaidyanathan, P. P.0000-0003-3003-7042
Additional Information:© 2007 IEEE. Issue Date: 4-7 Nov. 2007; Date of Current Version: 11 April 2008. This work was supported in part by the NSF grant CCF-0636799.
Funders:
Funding AgencyGrant Number
NSFCCF-0636799
Other Numbering System:
Other Numbering System NameOther Numbering System ID
INSPEC Accession Number9941469
DOI:10.1109/ACSSC.2007.4487161
Record Number:CaltechAUTHORS:20100825-133532010
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20100825-133532010
Official Citation:Byung-Jun Yoon; Vaidyanathan, P.P.; , "Fast Structural Similarity Search of Noncoding RNAs Based on Matched Filtering of Stem Patterns," Signals, Systems and Computers, 2007. ACSSC 2007. Conference Record of the Forty-First Asilomar Conference on , vol., no., pp.44-48, 4-7 Nov. 2007 doi: 10.1109/ACSSC.2007.4487161 URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4487161&isnumber=4487143
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:19661
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:26 Aug 2010 20:48
Last Modified:08 Nov 2021 23:54

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