On the art of identifying effective and specific siRNAs

Nature Methods - 3, 670 - 676 (2006) Published online: 23 August 2006; doi:10.1038/nmeth911

Yi Pei & Thomas Tuschl

Table 1 Representative siRNA sequence selection web tools
Tools
URLs
Comments
siDESIGN
http://www.dharmacon.com/
Scores and ranks candidate siRNAs based on thermodynamic and sequence-related criteria. BLAST search is conducted by default.

RNAi Designer
https://rnaidesigner.invitrogen.com/rnaiexpress/
Ranks candidate siRNAs using a primitive scoring system. BLAST search is automatic and the results are shown.

BIOPREDsi
http://www.biopredsi.org
An artificial neural network–based tool, which was trained with 2,500 experimentally assessed siRNAs. Analysis of genome-wide specificity is included.

Whitehead siRNA Selection server
http://jura.wi.mit.edu/bioc/siRNA
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.

siDE
http://side.bioinfo.ochoa.fib.es/
Developed for high-throughput applications of siRNAs using several published algorithms for efficacy prediction and a nonredundant database for specificity analysis.

siSearch
http://sisearch.cgb.ki.se/
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.

Sirna
http://sfold.wadsworth.org/sirna.pl
Sequence selection tool, which incorporates the target accessibility in the evaluation. No specificity analysis.

siRNA design software
http://www.cs.hku.hk/sirna
Candidate siRNAs proposed by various previously developed sequence selection tools are classified based on target accessibility.