CoreBoost / CoreBoost_HM
CoreBoost is a program for predicting the location of transcription start sites for human polymerase II promoters. It is based on two classifiers, one for CpG related promoters and the other for non-CpG related promoters. Both classifiers apply boosting techniques with stumps and select important small scale as well as large scale sequence features such as position specific core promoter elements and the flexibility of promoter sequences. The current version has more than 30% sensitivity and positive predictive value at 50 bp resolution.
CoreBoost_HMis a program for predicting the location of human polymerase II (Pol II) core-promoters. It is developed based on human Pol II core-promoter predictor CoreBoost by integrating specific histone modification profiles and the DNA sequence features together. Same as Coreboost, CoreBoost_HM is based on two classifiers, one for CpG related promoters and the other for non-CpG related promoters. Both classifiers apply boosting techniques with stumps and select important sequence features and histone modification features. Our analysis suggested that integrating histone modification profiles can provide much higher sensitivity, specificity and high resolution for human core-promoter prediction.
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Boosting with stumps for predicting transcription start sites.
Zhao X, Xuan Z, Zhang MQ.
Genome Biol. 2007;8(2):R17.
High-resolution human core-promoter prediction with CoreBoost_HM.
Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ.
Genome Res. 2009 Feb;19(2):266-75. Epub 2008 Nov 7.