McPromoter MM:II -- The Markov Chain Promoter Prediction Server
Duke University, Institute for Genome Sciences and Policy

A statistical tool for the prediction of transcription start sites in eukaryotic DNA

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This is the McPromoter site at Duke. This is the 2002 version of McPromoter. The older versions have been retired. Please visit our updated version for Drosophila sequences.
The human version is currently not developed further.

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".

Submission by pasting a single sequence:

McPromoter was developed by Uwe Ohler while at the University of Erlangen-Nuremberg, with help from Georg Stemmer, Andreas Kulicke. The software is copyright © 1999--2001 by Uwe Ohler, 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!"