George Mason University     |      Departments of MMB & Mathematics

Frequently Asked Questions

Q: Why do I need TREESORT prediction of the siRNA seats at all ?

A: Because conventional siRNA designing softwares do not include prediction of the off-target hybridization. After the completion of the designing step, one shall perform the similarity search with the basic local alignment search tool (BLAST) or using an exhaustive Smith-Waterman local alignment algorithm. If one of these searches results in off-target, predicted siRNA shall be scraped and siRNA design shall start form scratch. Upfront siRNA seat calculation with TREESORT database guarantees minimized off-target hybridization at the pre-design stage.

Q: Why I have to use conventional siRNA design program after I completed predictions of the siRNA seats by TREESORT ?

A: TREESORT is a pre-design tool, it helps to minimize possibilities for the successful siRNA prediction. After downloading a set of siRNA seats, you may employ conventional siRNA design program that will check candidate siRNAs for a low G+C content, a lack of internal repeats, an A/U-rich 5' end, certain secondary structures at the siRNA target site and other features. Use of the pre-design programs improves results of the subsequent use of the conventional siRNA design algorithms [Alsheddi et al., 2009]. PMID: 18389634. (

Q: Where can I read about dangers of the off-target hybridization ?

A: There are a number of publications that cover this topic. For example, please see an excellent review by Jackson and Linsley published in Nature Review Drug Discovery in 2010. PMID: 20043028 (

Q: Where I can find conventional siRNA desing software available for free ?

A: There are a number of resources freely available on the web. For example you may want to follow one of these links: