The REPuter Program Family

• REPfind
  • detects degenerate repeats with insertions, deletions, mismatches
  • detects direct repeats as well as reverse complemented
  • output size: control via parameters for min. length and max. error
  • these parameters can also be calculated heuristically by the program, according to the number of repeats required by the user
  • output is sorted by significance scores (E-values, as in BLAST)
• REPselect
  • selects interesting repeats from the output of REPfind as specified by user-defined criteria
  • delivers a list of repeats of chosen length, degeneracy or significance
  • simple interfacing to other
  • analysis program via executable object code that is linked dynamically
• REPvis
  • state of the art interactive visualization tool to display large amount of repeats data
  • designed to be used by the biologist, thus putting the data in the hands of those who can best interpret it
  • written in ANSI C using GTK
  • overview of the repeats over whole genome / chromosome
  • repeats displayed as lines connecting their starting positions
  • further display modes: circular graph and dot plot
  • color coded repeat lengths and significance scores
  • scroll bar controls amount of data displayed
  • zoom function to display details of a particular repetitive region
  • single repeat can be selected to view the alignment
  • submit corresponding nucleotide sequence to FASTA / BLAST
  • subsequences can be exported to a file
  • display additional user provided annotation
  • batch mode to produce publishable graphic of repeat structure

The REPuter programs are freely available for universities. Get the appropriate license here:

Postscript format.

PDF format.