A Web-based design center for vector-based siRNA and siRNA cassette
A Web-based design center for vector-based siRNA and siRNA cassette
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DOI：
10.1093/bioinformatics/bth164
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发表时间：
2004-07
期刊：
影响因子：
5.8
通讯作者：
Luquan Wang;Forest Y. Mu
中科院分区：
文献类型：
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作者：
Luquan Wang;Forest Y. Mu
为了促进基于载体的siRNA和siRNA盒的设计过程，已经开发了由siRNA靶标发现器、siRNA构建体构建器和siRNA序列加扰器组成的工具集。使用siRNA靶标查找器来鉴定候选siRNA靶位点。该程序自动进行同源性过滤，最大限度地减少非特异性交叉反应，根据RNA双链体内部稳定性和siRNA正义/反义链二级结构过滤靶位点。siRNA构建体构建体用于产生作为载体插入物或盒插入物的siRNA发夹构建体。siRNA序列加扰器用于产生siRNA实验的阴性对照序列。总之，这些程序提供了一个全面的实用程序集，以解决基于DNA的siRNA设计的特定生物信息学需求。基于Web的设计工具可在GenScript网站（siRNA设计中心）上获得。http://www.genscript.com或http://www.genscript.com/rnai.html#design或http://www.genscript.com/sirna_ca.html#design
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