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Bioinformatics Vol. 19 Suppl. 1 2003
Pages i34-i43
© 2003 Oxford University Press

Predicting bacterial transcription units using sequence and expression data

Joseph Bockhorst 1,2,*, Yu Qiu 3, Jeremy Glasner 3, Mingzhu Liu 3, Frederick Blattner 3 and Mark Craven 2,1

1 Department of Computer Sciences
2 Department of Biostatistics & Medical Informatics
3 Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA

Received on January 6, 2003 ; accepted on February 20, 2003

Motivation: A key aspect of elucidating gene regulation in bacterial genomes is identifying the basic units of transcription. We present a method, based on probabilistic language models, that we apply to predict operons, promoters and terminators in the genome of Escherichia coli K-12. Our approach has two key properties: (i) it provides a coherent set of predictions for related regulatory elements of various types and (ii) it takes advantage of both DNA sequence and gene expression data, including expression measurements from inter-genic probes.

Results: Our experimental results show that we are able to predict operons and localize promoters and terminators with high accuracy. Moreover, our models that use both sequence and expression data are more accurate than those that use only one of these two data sources.

Availability: Our E.coli transcription-unit predictions are available from http://www.biostat.wisc.edu/gene-regulation/

Contact: joebock{at}biostat.wisc.edu; craven{at}biostat.wisc.edu

* To whom correspondence should be addressed.


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