RepeatFinder project is a console-based bioinformatics tool that searches for repeating stretches of DNA.
It allows mismatches, but enforces a one to one mapping between sections of DNA and a repeat motif, meaning that a section of DNA cannot be associated with more than one match.
RepeatFinder, after a couple of years of private lab use, is now available for public consumption!
RepeatFinder is a tool for finding repeating segments of DNA called motifs and then parsing them so that no repeating segments overlap - it is an exclusive matching algorithm where any part of the original DNA string is associated with one and only one match.
RepeatFinder has been written to compile and run on Linux and Windows. The source code has been designed to have a minimum of requirements so if you can compile a C program, then hopefully RepeatFinder will work for you even if your OS isn't one of the above. Let me know if you succesfully compile RepeatFinder on another platform.
Further details about the algorithm and how to use the command line tools will be added to this site in due time. In the mean time the first release, 1.0.0, is available for download here. Only source, x86 and x64 linux binaries are currently available. Windows binaries coming soon!