[Biodevelopers] Looking for repeat motifs - ideas?

[Michael Nuhn]

Hi, Jeff!

> What threshold would you use for gaps and mismatches?

I would look for about 1 mismatch in the repeat and a gap of about 4-6bp.
But that can vary a bit. The bigger picture for me is to not only look for
the one case but to make a tool that can do similar searches and is easy to
use.

I have started here:
http://nbc11.biologie.uni-kl.de/motifsearch2/index.pl (Link may change in
the future)

>If you can have any
>number of mismatches within the motif and
>any size gap, it becomes more of
>problem in pattern recognition.

The whole thing is geared more to find candidates for sequences that
regulate transcription. No pathological cases. ;-)

Cheers,
Michael.