Rapid match-searching for gene silencing assessment

Horn, M. E. T. & Waterhouse, P. M. (2010) Rapid match-searching for gene silencing assessment. Bioinformatics, 26(16), pp. 1932-1937.

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Abstract

Motivation: Gene silencing, also called RNA interference, requires reliable assessment of silencer impacts. A critical task is to find matches between silencer oligomers and sites in the genome, in accordance with one-to-many matching rules (G-U matching, with provision for mismatches). Fast search algorithms are required to support silencer impact assessments in procedures for designing effective silencer sequences.Results: The article presents a matching algorithm and data structures specialized for matching searches, including a kernel procedure that addresses a Boolean version of the database task called the skyline search. Besides exact matches, the algorithm is extended to allow for the location-specific mismatches applicable in plants. Computational tests show that the algorithm is significantly faster than suffix-tree alternatives. © The Author 2010. Published by Oxford University Press. All rights reserved.

Impact and interest:

4 citations in Scopus
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4 citations in Web of Science®

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ID Code: 65853
Item Type: Journal Article
Refereed: Yes
Additional Information: Articles free to read on journal website after 12 months
Additional URLs:
Keywords: untranslated RNA, algorithm, article, chemistry, computer program, genome, nucleic acid database, RNA interference, Algorithms, Databases, Nucleic Acid, RNA, Untranslated, Software, OA via Highwire Press
DOI: 10.1093/bioinformatics/btq318
ISSN: 13674803
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > PLANT BIOLOGY (060700)
Divisions: Current > Schools > School of Earth, Environmental & Biological Sciences
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Oxford University Press
Deposited On: 08 Jan 2014 04:55
Last Modified: 22 Jan 2015 06:14

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