Method

Boosting with stumps for predicting transcription start sites

Xiaoyue Zhao , Zhenyu Xuan and Michael Q Zhang

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

author email corresponding author email

Genome Biology 2007, 8:R17doi:10.1186/gb-2007-8-2-r17

Published:	2 February 2007

Subject areas: Bioinformatics, Molecular biology, Genome studies

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.