Dear Peter,

siRNA designing tool such as:

• siDirect 2.0 (Naito et al., 2009), (http://sidirect2.rnai.jp/)

• sirna wizard, (http://www.sirnawizard.com/design.php)

• Dharmacon siRNA designing tool, (http://www.dharmacon.com/designcenter/designcenterpage.aspx)

• White head siRNA designing tool (http://sirna.wi.mit.edu/home.php) &

• Genscript siRNA software http://www.genscript.com/gsfiles/flash/siRNA.swf

I personally like siDirect 2.0, it has a best algorithm, but for some criteria you have to analysis by other tools to design or optimize the perfect siRNA. Also please read the article of Naito et al. 2009, for deep knowledge on their used algorithm.

Regards

NAyem ZObayer

What's your study system?

Mammalian cell lines

I also use siDirect 2.0. The good side of this program is that you can choose which algorithm you would like to use (Ui-tei, Reynolds, Amarzguioui or a combination of any of those three).

You can also choose seed stability, CG content and etc.

If it is your first time designing siRNAs I suggest take a look at the papers from authors above (all from 2004).

ShRNAPred 1.0 is an open source shRNA designing tool you can get the software from the following link.

http://bioinformatics.iasri.res.in/EDA/downloads/shRNAPred_v1.0.exe/

Integrated DNA Technologies (IDT) has a couple of useful tools:

1) http://www.idtdna.com/Scitools/Applications/RNAi/RNAi.aspx?source=menu

2) http://www.idtdna.com/Scitools/Applications/shRNA/

Just a quick update on the Dharmacon tool/algorithm. The siDESIGN Center can now be found on the new (since Oct 2012) Thermo Scientific Biosciences website, here:

http://www.thermoscientificbio.com/design-center/

Also, while the basis of the siDESIGN Center was the Reynolds algorithm, our bioinformatics and research scientists have gone well beyond the original 8 criteria to further refine the algorithm over the years for efficient siRNA design.

Many thanks for your valuable contributions.

Just throwing something in that I didn't see covered:

BLOCK-iT™ RNAi Designer by Life/Invitrogen

http://rnaidesigner.lifetechnologies.com/rnaiexpress/

Good Luck :)