I re[cently asked about help finding promoters in particular][1], and got a helpful pointer for that... however, it wasn't exactly what I wanted I found out.

I then found something much closer to what I wanted: the [Integrated Genome Viewer has a "Motif Finder"][2] tool, and you can even enter in ambiguous nucleotides to it.  The only catch (for me at least) is... is there a command line tool like it?  Do I have to interact with IGV through the GUI?  It seems there is some command line support for IGV, [but it seems like it is geared more for pre-processing][3].  Sorry if I missed something though, would appreciate any pointers!


  [1]: http://%20https://www.biostars.org/p/484669/#484737
  [2]: https://software.broadinstitute.org/software/igv/motif_finder
  [3]: https://software.broadinstitute.org/software/igv/igvtools_commandline
If any useful, I wrote [fastaRegexFinder](https://github.com/dariober/bioinformatics-cafe/tree/master/fastaRegexFinder) for this.