Status of siRNA Design Software

Version	Release Date	Features
3	17th April, 2005	Instead of pasting an mRNA sequence, an option to input the accession number of an mRNA sequence is provided. A parameter to specify the organism is added so that other design tools can make use of it for blasting. Apart from ranking the siRNA candidates by popularity where each software is weighted equally, another option for ranking the candidates -- weighted popularity -- is provided. Each software is given a different weight, depending on the number of candidates reported by the software. The more the number of candidates reported by a software is, the smaller is the weight. Our implementation of a design tool based on the design guidelines of Tuschl et al. + rational design of Reynolds et al. A guestbook to collect some feedbacks from our users on the usefulness and effectiveness of our tool. A database to store the known effective siRNAs and ineffective siRNAs w.r.t. an mRNA, with the help of our users who are willing to share their experimental results with the community. Some bugs have been fixed.
2	16th Jan, 2005	The software tool now supports 11 design tools. Apart from the tools that are based on the design guidelines of Tuschl et al., tools that are based on the rational design of Reynolds et al. are also included. Here is a list of the newly added tools: Dharmacon siDESIGN Center GenScript siRNA Target Finder Qiagen siRNA Design Tool siDirect Invitrogen BLOCK-iT RNAi Designer Deqor An option is provided to run mfold on behalf of the users. An improved output format of the siRNA candidates to distinguish between the core 19-nt and the overhang. Some bugs have been fixed.
1	27th August, 2004	A software tool that provides a unified platform for finding siRNA candidates. Currently, it supports 5 design tools: Ambion siRNA Target Finder Jack Lin's siRNA Sequence Finder OptiRNAi Emboss siRNA Our implementation of the design guidelines based on Tuschl et al. A utility for filtering ineffective siRNAs reported by the software tools.