Discriminatively search for a motif of a given length using given nucleotide sequences
โ At least that's what it says on the box...
This is part of a project I worked on in highschool. I thought I'd just throw this here as backup.
The idea was to write a relatively fast and simple motif finder. The result is a working, semi-accurate command line program that can find motifs in genetic data if you mess with its options for long enough.
I don't really remember what packages are needed, but I developed it on Linux a few years ago, and got it working on OS X not so long ago, so given the right packages, this should work on either system.
It seems to require the following packages (though a few more might be needed):
GD::Graph
Math::GSL
Text::LevenshteinXS
The related paper should be somewhere on the Internet, I'll attach a link when I find it.