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


BACKGROUND
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
Wang
Luquan
L
GenScript Corporation, 120 Centennial Avenue, Piscataway, NJ 08854, USA. larryw@genscript.com
Mu
Forest Y
FY
D017076:Computer-Aided Design; D005822:Genetic Vectors / Q000737:chemistry* / Q000235:genetics; D020407:Internet; D016254:Mutagenesis, Insertional / Q000379:methods*; D009862:Online Systems; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D034741:RNA, Small Interfering