Fast Computation of Maximal Repeats in Complete Genomes Kurtz, Schleiermacher S. Kurtz and C. Schleiermacher: REPuter - Fast Computation of Maximal Repeats in Complete Genomes, Bioinformatics, Vol. 15(5), 1999 motifs nucleic:motifs nucleic:repeats reputer reputer perl "reputer" 0 fmt perl " tr -d \\"\\\\\\\\n\\" < $seq > $seq.raw ; " -10 rawfile *.raw seq Sequence File perl " $seq.raw " 10 13 search Search options 1 leastlength Length a maximal repeat must have to be reported (-l) perl " -l $value" 5 forward Report all maximal forward repeats (-f) perl ($value)? " -f":"" 1 reverse Report all maximal reverse repeats (-r) perl ($value)? " -r":"" 1 complemented Report all maximal complemented repeats (-c) perl ($value)? " -c":"" 1 revcomp Report all maximal reversed and complemented repeats (-x) perl ($value)? " -x":"" 1 report Report options 1 substring Report the repeated substrings (-s) perl ($value)? " -s":"" 1 max Maximal number of repeats reported (-o) perl ($value)? " -o $value":"" 1 stat Give only statistics about the length of different repeats found (-p) perl ($value)? " -p":"" 1 -s and -p options cannot be combined