RNAxs is a tool especially created to design potent siRNAs. The webserver version can be found here, while a standalone version can be downloaded from here. The standalone version was tested only on linux. depends on the latest version of the ViennaRNA package as well as on the Algorithm::Diff perl module. The main advantage of the standalone version is that siRNAs can be designed for more than one sequence at a time. RNAxs can further help to design siRNAs that downregulates all sequences in a list. This is useful when homolog genes or alternatively spliced transcriped should be targeted by the same siRNA. It can also design siRNAs that are specific to each sequences in a sequence file. This is helpful when only one splice variant should be downregulated. Finally the standalone version of RNAplex can also rank a list of siRNAs coming from another siRNA design tool. For more information please look at the documentation perldoc -F ./ An example file can be found here. siRNAs downregulating all sequences in the file are found here, while a the set of sequence specific siRNAs can be found here here . For any further question do not hestitate to contact me.