[Biodevelopers] Looking for repeat motifs - ideas?

[Michael Nuhn]

Hello, Everyone!

I am looking for a program that can find short repeats with some mismatches
and a certain distance between them. Something like this:

TTTAAG GCGC TTTAAG

where the actual sequence of the repeat (TTTAAG) is unknown in advance and
may have mismatches to the repeat.

Repeat finders I know about are optimized for searching for large repeats
anywhere on the entire sequence. That would not be useful to me since it
would create an abundance of matches like this: TTTAAG [ca. 300 000 bases
here and then the second] TTTAAG. Others only look for tandem repeats, so
they would find  TTTAAG TTTAAG but not TTTAAG GCGC TTTAAG

The closest thing I could find is the program rnabob. It is really cool, but
rnabob seems only to be able to find inverted repeats, not normal repeats.

Does anyone know a program that can solve my problem? Help would be greatly
appreciated.

Thanks in advance,
Michael.

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Dipl.-Inform. Michael Nuhn
Bioinformatik
Zentrum für Nanostrukturtechnologie und
Molekularbiologische Technologie

+49 (0)631 - 205 4334
nuhn at rhrk.uni-kl.de
http://nbc3.biologie.uni-kl.de/
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