Summary
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. RNAxs.pl 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 ./RNAxs.pl. 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.