title: Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms.
abstract: RNAi interference and siRNA have become useful tools for investigation of gene function. However, the discovery that not all siRNA are equally efficient made necessary screens or design algorithms to obtain high activity siRNA candidates. Several algorithms have been published, but they remain inefficient, obscure, or commercially restricted. This article describes an open-source JAVA program that is surprisingly efficient at predicting active siRNAs (Pearson correlation coefficient r = 0.52, n = 526 siRNAs). Furthermore, this version 1.0 sets the stage for further improvement of the free code by the open-source community (http://sourceforge.net/).
authors.affiliation: Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. torgeir.holen@medisin.uio.no
authors.forename: Torgeir
authors.initials: T
authors.lastname: Holen
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D011237:Predictive Value of Tests; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D034741:RNA, Small Interfering