Copy of original repeat_finder.pl
The copy of repeat_finder.pl found here is only for backup purposes. All kudos go to the original authors of the program.
The our best knowledge this program was first refered to by Redfield et al. in Redfield RJ, Findlay WA, Bosse J, Kroll JS, Cameron AD, et al. (2006) Evolution of competence and DNA uptake specificity in the Pasteurellaceae. BMC Evol Biol 6: 82. (https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-6-82) and formally available at NRC Institute for Biological Sciences: Genomics and Proteomics. [http://ibs-isb.nrc-cnrc.gc.ca/glycobiology/group_software_e.html]
We used this program and refered to it in "Dialects of the DNA uptake sequence in Neisseriaceae". (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003458)
March 2020, S.A. Frye
Original program information taken form the Perl script:
Name: repeat_finder
Purpose: Searches for DNA repeats in a sequence. It searches for every permutation of an n-mer, and reports the number of hits.
Author: John Nash
Copyright (c) National Research Council of Canada, 2002, all rights reserved.
Licence: This script may be used freely as long as no fee is charged for use, and as long as the author/copyright attributions are not removed.
History: 4-12 July 2002: Alpha versions.
Thanks: To Ed Taboada for suggesting hashing the repeats
To-do: Put ranges in for command line switches