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Open Access Software

Design and evaluation of genome-wide libraries for RNA interference screens

Thomas Horn12, Thomas Sandmann13 and Michael Boutros1*

Author Affiliations

1 German Cancer Research Center (DKFZ), Div. of Signaling and Functional Genomics and University of Heidelberg, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany

2 University of Heidelberg, Hartmut Hoffman-Berling International Graduate School for Molecular and Cellular Biology, D-69120 Heidelberg, Germany

3 University of Heidelberg, CellNetworks Cluster of Excellence, D-69120 Heidelberg, Germany

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Genome Biology 2010, 11:R61  doi:10.1186/gb-2010-11-6-r61

Published: 15 June 2010

Abstract

RNA interference (RNAi) screens have enabled the systematic analysis of many biological processes in cultured cells and whole organisms. The success of such screens and the interpretation of the data depend on the stringent design of RNAi libraries. We describe and validate NEXT-RNAi, a software for the automated design and evaluation of RNAi sequences on a genome-wide scale. NEXT-RNAi is implemented as open-source software and is accessible at http://www.nextrnai.org/. webcite