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Briefings in Bioinformatics Advance Access published online on June 16, 2009
Briefings in Bioinformatics, doi:10.1093/bib/bbp027
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Towards accurate human promoter recognition: a review of currently used sequence features and classification methods

Jia Zeng, Shanfeng Zhu and Hong Yan

Corresponding author. Jia Zeng, Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong. Tel: +852 34117636; Fax: +852 34117892; E-mail: j.zeng{at}ieee.org


Jia Zeng has a PhD in pattern recognition from the City University of Hong Kong. He is a Member of the IEEE.


Shanfeng Zhu has a PhD in information retrieval from the City University of Hong Kong.


Hong Yan has a PhD in electrical engineering from the Yale University. He is a fellow of the IEEE, IAPR and IEAust.

This review describes important advances that have been made during the past decade for genome-wide human promoter recognition. Interest in promoter recognition algorithms on a genome-wide scale is worldwide and touches on a number of practical systems that are important in analysis of gene regulation and in genome annotation without experimental support of ESTs, cDNAs or mRNAs. The main focus of this review is on feature extraction and model selection for accurate human promoter recognition, with descriptions of what they are, what has been accomplished, and what remains to be done.

Keywords: human promoter recognition, genome annotation, feature extraction, model selection

Submitted: February 19, 2009. Received (in revised form): May 3, 2009.


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