Table 2.

Tools for siRNA design

Tool	Param	sh	as	Therm	Off	Link
OptiRNAi 2.0	✕	✕	✕	✕	✕	http://rnai.nci.nih.gov
siDirect 2	✕	✕	✔	✔	✔	http://sidirect2.rnai.jp
siRNA scales	✕	✕	✔	✕	✕	http://gesteland.genetics.utah.edu/siRNA_scales
siExplorer	✕	✕	✔	✕	✔	http://rna.chem.t.u-tokyo.ac.jp/cgi/siexplorer.htm
RFRCDB-siRNA	✕	✕	✔	✕	✔	http://www.bioinf.seu.edu.cn/siRNA/index.htm
OligoWalk	✕	✕	✔	✔	✕	http://rna.urmc.rochester.edu/cgi-bin/server_exe/oligowalk/oligowalk_form.cgi
Sfold	✔	✕	✔	✔	✕	http://sfold.wadsworth.org
siMAX	✔	✕	✔	✔	✔	http://www.operon.com/products/siRNA/sirna-overview.aspx
DSIR	✔	✔	✔	✕	✔	http://biodev.cea.fr/DSIR/
siRNA scan	✔	✕	✔	✕	✔	http://bioinfo2.noble.org/RNAiScan.htm
RNAxs	✔	✕	✔	✔	✔	http://rna.tbi.univie.ac.at/cgi-bin/RNAxs
i-Score	✔	✕	✔	✔	✕	http://www.med.nagoya-u.ac.jp/neurogenetics/i_Score/i_score.html
siVirus	✔	✕	✕	✕	✔	http://sivirus.rnai.jp

Details and links are given for each tool. Param: it is possible to provide parameters and constraints as input. sh: the tool also returns the complete shRNA sequence. as: both antisense and sense siRNA sequences are returned. Therm: the tool takes into account thermodynamic features. Off: the tool performs or has the option for the computation of off-target sequences for the designed siRNAs