Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms.

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/).

[1]  S. Jayasena,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

[2]  M. Amarzguioui,et al.  Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. , 2002, Nucleic acids research.

[3]  A. Reynolds,et al.  Rational siRNA design for RNA interference , 2004, Nature Biotechnology.

[4]  K Taira,et al.  siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cells , 2003, Nucleic acids research.

[5]  Tomoyuki Yamada,et al.  siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference , 2004, Nucleic Acids Res..

[6]  Ola Snøve,et al.  A comparison of siRNA efficacy predictors. , 2004, Biochemical and biophysical research communications.

[7]  Dieter Huesken,et al.  Design of a genome-wide siRNA library using an artificial neural network , 2005, Nature Biotechnology.

[8]  Andreas Henschel,et al.  DEQOR: a web-based tool for the design and quality control of siRNAs , 2004, Nucleic Acids Res..

[9]  T. Du,et al.  Asymmetry in the Assembly of the RNAi Enzyme Complex , 2003, Cell.

[10]  K. Ui-Tei,et al.  Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. , 2004, Nucleic acids research.

[11]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[12]  A. Fire,et al.  Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Thomas Tuschl,et al.  Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. , 2003, Antisense & nucleic acid drug development.

[14]  Ola Snøve,et al.  Many commonly used siRNAs risk off-target activity. , 2004, Biochemical and biophysical research communications.

[15]  M. Amarzguioui,et al.  An algorithm for selection of functional siRNA sequences. , 2004, Biochemical and biophysical research communications.

[16]  C. F. Bennett,et al.  Efficient Reduction of Target RNAs by Small Interfering RNA and RNase H-dependent Antisense Agents , 2003, The Journal of Biological Chemistry.

[17]  T. Tuschl,et al.  Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate , 2001, The EMBO journal.

[18]  Xin Zheng,et al.  BIOINFORMATICSAPPLICATIONS NOTE doi:10.1093/bioinformatics/btl026 Databases and ontologies , 2005 .

[19]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[20]  Pierre Baldi,et al.  Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..

[21]  O. Ottersen,et al.  Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo , 2005, Nucleic acids research.

[22]  T. Tuschl,et al.  RNA interference is mediated by 21- and 22-nucleotide RNAs. , 2001, Genes & development.