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.
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.
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|Item Type:||Journal Article|
|Additional Information:||Articles free to read on journal website after 12 months|
|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|
|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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