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- esperr: a newer version of the "regulatory potential" program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)
- 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