It would help to know little about why you need a design algorithm. If it is for a species that does not have commercially available products then it is your only choice. If you ultimately want an sh then you have to be concerned about an si algorithm that may fall short designing sh. A good si design does not always make a good sh design. So, you may have to endure some testing to see which works the best.

If you are looking for human or mouse si/sh it may be best to go with a commercially available product. Then you at least get technical support to help (if that is something you need). If you are looking for sh, there was recently a paper out of Greg Hannon's lab "Functional identification of optimized RNAi triggers using a massively parallel Sensor assay" that describes their process for finding optimal shRNA sequences. The algorithm developed from this is not yet available, but they functionally tested 270,000 designs in their screen to create the training data set (20,000 are from the paper). There is a new company that sells their shRNA-mir collections for human and mouse called Transomic Technologies. Disclaimer, I work for this company.

It is interesting that you mention you get different sequence targets for the si designs. It is true if you look at shRNA designs as well. There is very little overlap between the shRNA library designs as well.

The tricky part is that most of these design tools will probably try to make an shRNA that will knock down one specific mRNA variant (NM_...). What you probably really want is an shRNA that will knock down all mRNA variants of your gene. GeneCopoeia has a nice catalog offer where they will send you 4 shRNAs each complementary to different sites within the open reading frame, so you can test all 4 to see if they knock down all of the mRNA variants you need to eliminate. Here's an example: http://www.genecopoeia.com/product/search/detail.php?prt=11&cid=&key=HSH012557

Have you tried the siMAX siRNA Design Tool? The results are according to the Reynolds, UI-Tei and DSIR scores.

https://www.eurofinsgenomics.eu/en/dna-rna-oligonucleotides/oligo-tools/sirna-design-tool/

Hi! Take a look at this tool:

Article SSD - a free software for designing multimeric mono-, bi- an...

http://www.rnaiweb.com/RNAi/RNAi_Web_Resources/RNAi_Tools__Software/Online_siRNA_Design_Tools/shRNA_Design/index.html

http://biosettia.com/support/shrna-designer/

Choosing the best siRNA (small interfering RNA) designer tool, especially for shRNA (short hairpin RNA) applications, can depend on various factors such as the specific requirements of your experiment, ease of use, accuracy, and the algorithms used for siRNA prediction. As of my last update in April 2023, several notable tools are commonly used in the field:

When choosing a tool, consider the following:

• Target Specificity: Ensuring minimal off-target effects.
• Efficacy of siRNA: The tool should predict siRNAs with high gene silencing potential.
• Algorithm and Database: Look for tools that are regularly updated and use robust algorithms.
• User Interface: Ease of use can be a critical factor, especially for beginners.

It's always beneficial to review recent literature and research findings, as the field of RNA interference is rapidly evolving. Additionally, consulting with peers or experts who have practical experience in RNAi experiments can provide valuable insights into the most effective and user-friendly tools currently available.

l Reviewing the protocols listed here may offer further guidance in addressing this issue.