The Drosophila release 3 genome special issue of Genome Biology, including a genome-wide
analysis of Drosophila core promoters and McPromoter predictions,
has been published
here!
Read the
Q & A site first
for information about the recent changes and instructions how to use McPromoter!
(Also contains links to the McPromoter papers and Uwe's thesis.)
Sensitivity and specificity are now at about 40-50% for both vertebrate
and Drosophila at the transcript level .
Hint: If you don't get a prediction, have a look at the
graphics that comes with the email to find optima
that might have been missed by the pre-specified sensitivity level.
Note for Drosophila: If you want to retrieve predictions for a large fly region, use the GadFly analysis interface. Type in a chromosome arm under "Query sequence" (either 2L, 2R, 3L, 3R, 4, or X), and choose "promoter" as Program. This will give you all predictions in this arm with scores over 0.85, without any filtering for repeats or low-complexity. For specific regions, these predictions also show up in the FlyBase Genome Browser, if you choose "Dump view as TABLE" in the "display settings".
McPromoter was developed by Uwe Ohler at the University of Erlangen-Nuremberg,
with help from Georg Stemmer, Andreas Kulicke.
The software is copyright © 1999--2001 by University of Erlangen-Nuremberg
(Chair for Pattern
Recognition). All rights are reserved.
Problems, Comments? email to Uwe Ohler
Neural networks courtesy of
Stuttgart
Neural Network Simulator SNNS
Our favourite user comment:
"I'll have a McPromoter, a pack of
enhancers and a TATA box, to go!"