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Bioinformatics Advance Access originally published online on March 4, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Applications Note

A Web-based design center for vector-based siRNA and siRNA cassette

Luquan Wang * and Forest Y. Mu

GenScript Corporation, 120 Centennial Avenue, Piscataway, NJ 08854, USA

Received on November 18, 2003; revised on January 26, 2004; accepted on February 10, 2004

Summary: To facilitate the designing process for vector-based siRNA and siRNA cassette, a tool set has been developed consisting of a siRNA target finder, a siRNA construct builder and a siRNA sequence scrambler. The siRNA target finder is used to identify candidate siRNA target sites. The program automates homology filtering, minimizes non-specific cross-reaction, filters target sites based on RNA duplex internal stability and siRNA sense/anti-sense strand secondary structure. The siRNA construct builder is used to create a siRNA hairpin construct as a vector insert or a cassette insert. The siRNA sequence scrambler is used to generate a negative control sequence for siRNA experiments. Together, these programs provide a comprehensive utility set to address the specific bioinformatics need of DNA-based siRNA design.

Availability: The Web-based design tools are available at GenScript Website (siRNA design center). http://www.genscript.com or http://www.genscript.com/rnai.html#design or http://www.genscript.com/sirna_ca.html#design

Contact: larryw{at}genscript.com

* To whom correspondence should be addressed.


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