R'MES: Finding Exceptional Motifs in Sequences

Three possibilities exist to use R'MES:

through the dedicated web interface; note that all combinations of parameters are not available,
by downloading and installing the source distribution on your own computer (see Downloads section),
for the Migale facility users, R'MES tools are already available through command lines (to ask for a Migale account, complete this form).

R'MES package contains 4 tools:

rmes is the main program that computes the exceptionality score for all motifs, together with the observed count, the estimated expected count and the estimated variance count in the choosen Markov model (see the Running section).
rmes.format is important because it displays the results contained in an output file generated by the rmes command. It produces a table with the motifs sorted according to their exceptionality scores (see the Utilities section).
rmes.gfam can be useful if one wants to study degenerated motifs. It allows to generate word family files when the corresponding families are degenerated DNA motifs which can be written thanks to the bases a, c, g, t and n (see the Utilities section).
rmes.composition computes the length of a sequence and its composition (see the Utilities section).

Instead of using the command line rmes.format to display R'MES results as a table in a text file, it is possible to use an additional java graphical interface, RMESPlot, which is available at https://forgemia.inra.fr/sophie.schbath/rmesplot. It comes with its own user guide.