PLEXY is a tool for computation of optimal thermodynamical interactions of a box C/D snoRNA with a putative target RNA. It is based on RNAPLEX.


Be sure to have the latest version of RNAPLEX installed.
Executables of RNAPLEX should either be installed in the same directory or you have to provide the correct $PATH at the beginning

Input sequences

To perform a target prediction you have to provide: The header of each snoRNA sequence has to contain D- and/or Dprime- box annotation(s). The box annotation must be seperated with _ and have to be located at the end of the header line. The first two parts are taken for snoRNA_id, everything else does not matter at all.


Usage -o [directory/] -f [fa-file] -t|T [directory/|fa-file]


without -l option: (sorted, unique and nice)
./ -f U95.fa -o temp/ -T allTargets_human.fa -e -20.00
with -l option: (not sorted, not unique and not so nice, but machine readable and gentler to your memory, especially during runtime)
./ -f U95.fa -o temp/ -t /path/human_targetRNAs/ -e -20.00 -l


If you have any kind of problems or suggestions how to improve PLEXY feel free to send a mail to