SMaRTFinder is a command line tool to search biosequences for structured motifs (also known as structured models), that is, lists of patterns separated by distance intervals (gaps). It is based on an algorithm described in one of my publications and, although the code is not the best example of programming (at the time I didn’t know what C++ is), well, it works. It uses Kurtz’ suffix tree implementation for efficiently searching the given sequences.

It is released under the GPL license and it can be downloaded from the Applied Genomics Institute (IGA) web site.