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Open Access Method

Boosting with stumps for predicting transcription start sites

Xiaoyue Zhao, Zhenyu Xuan and Michael Q Zhang*

Author Affiliations

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA

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Genome Biology 2007, 8:R17  doi:10.1186/gb-2007-8-2-r17

Published: 2 February 2007

Abstract

Promoter prediction is a difficult but important problem in gene finding, and it is critical for elucidating the regulation of gene expression. We introduce a new promoter prediction program, CoreBoost, which applies a boosting technique with stumps to select important small-scale as well as large-scale features. CoreBoost improves greatly on locating transcription start sites. We also demonstrate that by further utilizing some tissue-specific information, better accuracy can be achieved.