RNA string kernels for RNAi off-target evaluation.
RNA interference (RNAi) is a posttranscriptional gene silencing mechanism used to study gene functions, knock down viral genes, and treat diseases therapeutically. However, an 'off-target effect' deteriorates its specificity and applicability. Complete off-target effects can only be characterised by examining each gene in a genome, which is too expensive to conduct experimentally and motivates a computational study. To simulate the sequence matching between an siRNA and its target mRNA allowing for mismatches, G-U wobbles and bulges, we propose string kernels and develop their efficient implementations for off-target detection. We evaluate RNAi specificities in Schizosaccharomyces pombe, Caenorhabdithis elegans, and human genomes.
Department of Computer Science, The University of New Mexico, Albuquerque, NM 87131, USA. sqiu@cs.unm.edu
Shibin
S
Qiu
Terran
T
Lane
D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D015894:Genome, Human; D006801:Humans; D015233:Models, Statistical; D012313:RNA / Q000737:chemistry*; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000737:chemistry; D034741:RNA, Small Interfering / Q000378:metabolism; D012568:Schizosaccharomyces / Q000378:metabolism; D012680:Sensitivity and Specificity; D012984:Software
D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering; D012313:RNA