Technique / Molecular Biology / RNAi siRNA gene silencing / siRNA design

Vector based siRNA design tool

Vector based siRNA design tool

Tools include:

*siRNA Target Finder: A software tool to identify unique candidate siRNA target sequence in your cDNA sequence.
* siRNA Construct Builder: A software tool to build small hairpin insert from siRNA target for expression vector.
* siRNA Sequence Scrambler: A software tool to create a scrambled sequence as negative control for your siRNA experiment.


Bioinformatics. 2004 Jul 22;20(11): 1818-20. A Web-based design center for vector-based siRNA and siRNA cassette.
Wang L, Mu FY.

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). or or

Last update 28-Aug-2006, Rating n/a of 1 votes.

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