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Title of Journal: J Supercomput

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Abbravation: The Journal of Supercomputing

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Springer US

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10.1002/chin.200446241

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1573-0484

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Efficient search algorithms for RNAi target detect

Authors: Shibin Qiu Terran Lane Cundong Yang
Publish Date: 2007/04/07
Volume: 42, Issue: 3, Pages: 303-319
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Abstract

RNA interference RNAi is a posttranscriptional gene silencing mechanism used to study gene functions inhibit viral activities and treat diseases therapeutically However RNAi has offtarget effects—nontarget genes can be unintentionally silenced Therefore target validation through target detection is crucial for the success of RNAi experiments Effective target detection must examine each gene expressed by an organism making computational efficiency a critical issue We develop efficient sequential and parallel search algorithms using RNA string kernels which model mismatches GU wobbles bulges and the seed region in the hybridization between an siRNA and its target mRNA Empirical results demonstrate that our algorithms achieved speedups of six orders of magnitude over the alignment algorithm based on tests in the organisms of S pombe C elegans D melanogaster and human Our design strategy also leads to a framework for efficient flexible and portable string search algorithms allowing for inexact matches

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