| siVirus:在线设计抗病毒siRNA的工具 | 点击： 作者： 来源： 时间： 2007-03-10 本站论坛
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|  | Nature Methods推荐的siRNA设计工具：
http://www.nature.com/nmeth/journal/v3/n9/abs/nmeth911.html;jsessionid=E4833004DB8CAC46620EEE7F94EBB663
siDESIGN
http://www.dharmacon.com/sidesign/default.aspx
特色：Scores and ranks candidate siRNAs based on thermodynamic and sequence-related criteria. BLAST search is conducted by default.
Ref:
6. Reynolds, A. et al. Rational siRNA design for RNA interference. Nat. Biotechnol. 22, 326–330 (2004).
79. Boese, Q. et al. Mechanistic insights aid computational short interfering RNA design. Methods Enzymol. 392, 73–96 (2005).
RNAi Designer
https://rnaidesigner.invitrogen.com/rnaiexpress/
特色：Ranks candidate siRNAs using a primitive scoring system.BLAST search is automatic and the results are shown.
Ref:
BIOPREDsi
http://www.biopredsi.org
特色：An artificial neural network–based tool, which was trained with ~2,500 experimentally assessed siRNAs. Analysis of genome-wide specificity is included.
Ref:
14. Huesken, D. et al. Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol. 23, 995–1001 (2005).
Whitehead siRNA Selection server
http://jura.wi.mit.edu/bioc/siRNA
特色：Offers flexibility in defining siRNA sequence patterns and selection of filter functions. Different properties of selected siRNAs are calculated, including thermodynamic values, polymorphisms are identified and the results of configurable BLAST search and filtering are shown. The user can sort the output in various ways and balance decisions.
Ref:
30. Yuan, B., Latek, R., Hossbach, M., Tuschl, T. & Lewitter, F. siRNA Selection Server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res. 32, W130–W134 (2004).
siDE
http://side.bioinfo.ochoa.fib.es/
特色：Developed for high-throughput applications of siRNAs using several published algorithms for efficacy prediction and a nonredundant database for specificity analysis.
Ref:
80. Santoyo, J., Vaquerizas, J.M. & Dopazo, J. Highly specific and accurate
selection of siRNAs for high-throughput functional assays. Bioinformatics 21,
1376–1382 (2005).
siSearch
http://sisearch.cgb.ki.se/
特色：The kernel algorithm focuses primarily on energy features of effective siRNAs. Alternative algorithms are also implemented
and integrated in the tool. siSearch is expandable to include newly discovered rules.
REF:
31. Chalk, A.M., Wahlestedt, C. & Sonnhammer, E.L. Improved and automated prediction of effective siRNA. Biochem. Biophys. Res. Commun. 319, 64–274(2004).
Sirna
http://sfold.wadsworth.org/sirna.pl
特色：Sequence selection tool, which incorporates the target accessibility in the evaluation. No specificity analysis.
Ref:
36. Ding, Y., Chan, C.Y. & Lawrence, C.E. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32, W135–W141(2004).
siRNA design software
http://www.cs.hku.hk/~sirna
特色：Candidate siRNAs proposed by various previously developed sequence selection tools are classified based on target accessibility.
Ref:
38. Yiu, S.M. et al. Filtering of ineffective siRNAs and improved siRNA design tool. Bioinformatics 21, 144–151 (2005).
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