Tregwiki:Predict promotor regions


 * Prediction of enhancers:
 * esperr: a newer version of the "regulatory potential" program
 * "Regulatory Pontential" track on UCSC: searches multiple alignments for transfac matches

Since there are now CAGE-data available from fantom2 and dbtss (included in UCSC?) I never really got into any detail for this topic. here are at least some keywords if you want to try this:
 * Prediction of promotors:
 * promoter explorer, a quite new addition compared to the others
 * NNPP: BGDP's prom prediction
 * [Promh] if you have two orthologous regions (oct 05: doesn't seem to work anymore)
 * EponineTSS
 * HexDiff
 * First EF: not really promotor prediction, rather First Exon Prediction, available on UCSC as a Track.
 * TSSG: rather old promoter predictor...


 * Note: Have a look at a very recent benchmark of promoter predictors done for Encode