NAME RepeatFinder - search for statistically significant, high-
complexity aminoacid repeats. SYNOPSIS RepeatFinder -f filename
[-b] [-d] [-e] [-s] [-g] [-j] [-r] [-l] [-t] DESCRIPTION
RepeatFinder is an ancillary program designed to automatize the
use the Gibbs sampler program (Neuwald et al., 1995) for the
detection of statistically significant, ungapped aminoacid
repeats. Input sequences need to be in fasta format. Detected
repeats are stored in the file 'result'. RepeatFinder runs the
Gibbs sampler program -g times searching for repeated modules
ranging in size between -b and -e aminoacids, using an increment
step of -s aminoacids. Only modules with a significance below -t
threshold are considered as significant. p-value of the
alignment is calculated according to the Karlin-Altschul
statistic (Karlin and Altschul, 1993). Sequences need to be of
length at least -l aminoacids in order to be analyzed. The
option -j allows to just count the input sequences. The option
-r can be used to restart the program aft