RNAduplex - Compute the structure upon hybridization of two RNA strands
RNAduplex [-e range] [standard_options] [<filename>]
RNAduplex reads two RNA sequences from stdin or <filename> and computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter-molecular base pairs, for the general case use RNAcofold.
The computed optimal and suboptimal structure are written to
stdout, one structure per line. Each line consist of: The structure
in dot bracket format with a "&" separating the two strands.
The range of the structure in the two sequences in the format
"from,to : from,to"; the energy of duplex structure in
The format is especially useful for computing the hybrid structure between a small probe sequence and a long target sequence.
For the standard options, such as -T, -4, -noGU, -noCloseGU, -P see the RNAfold man page.
Ivo Hofacker <firstname.lastname@example.org>