A motif searching program availalbe

Lemieux Sebastien lemieuse at ERE.UMontreal.CA
Mon Aug 28 06:49:11 EST 1995


ping at bnlux1.bnl.gov (Shiping Zhang) writes:

>I'm not sure if you meant to find consensus sequences.  There are
>programs doing that.  By definition, the so called motifs are explicitly
>defined or discovered patterns, which the program mentioned above
>searches in sequences.  One may come up with an algorithm to find motifs.
>But an algorithm is actually a set of rules which in turn must be
>explicitly defined.

Let's define a motif as a pattern that is believed to have some
significance due to its number of occurences higher than what would
have been expected by random distribution.

An other interesting application that could be found to such
hypothetical search engine would be to search for 3D structural motifs
in the structure database for significant patterns in the structure.
Mapping those motifs to the sequence pattern that produce them would
be of great significance to molecular modellers.

If any of you have insights about how that could be possible, I would
be willing to continue this discussion deeper by email...

ciao!

--
| Sebastien Lemieux, dept. biol.  ||  Look behind the wave of changes
| lemieuse at alize.ERE.UMontreal.CA ||  Feel the future taking shape
| PGP public key on finger.       ||  I can see the world to come (KJ)
  http://alize.ere.umontreal.ca/~lemieuse/




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