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Bioinformatics Advance Access published online on March 4, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth164
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received November 18, 2003
Revised January 26, 2004
Accepted February 10, 2004

Applications note

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

Luquan Wang 1* Forest Y. Mu 1

1 GenScript Corporation, 120 Centennial Ave., Piscataway, NJ 08854

* To whom correspondence should be addressed. E-mail: larryw{at}genscript.com.


  Abstract

To facilitate the designing process for vector-based siRNA and siRNA cassette, a tool set has been developed: siRNA target finder, siRNA construct builder, and 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 siRNA hairpin construct as vector insert or cassette insert. The siRNA sequence scrambler is used to generate 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

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