Tregwiki:Predict promotor regions

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    • esperr: a newer version of the "regulatory potential" program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