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  • esperr: a newer version of the "regulatory potential" program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

• Prediction of promotors:

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:

• • 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