Bioinformatics Vol. 17 no. 10 2001
Pages 878-889
© 2001 Oxford University Press
Detection of cis -element clusters in higher eukaryotic DNA
1 Bioinformatics Program, Boston University,
44 Cummington St
2 Department of Biology, Boston University,
5 Cummington St
3 Department of Biomedical Engineering,
Boston University, 44 Cummington St, Boston, MA 02215, USA
Received on April 20, 2001
; revised on July 6, 2001
; accepted on July 6, 2001
Motivation: Computational prediction and analysis of transcription regulatory regions in DNA sequences has the potential to accelerate greatly our understanding of how cellular processes are controlled. We present a hidden Markov model based method for detecting regulatory regions in DNA sequences, by searching for clusters of cis -elements.
Results: When applied to regulatory targets of the transcription factor LSF, this method achieves a sensitivity of 67%, while making one prediction per 33 kb of non-repetitive human genomic sequence. When applied to muscle specific regulatory regions, we obtain a sensitivity and prediction rate that compare favorably with one of the best alternative approaches. Our method, which we call Cister, can be used to predict different varieties of regulatory region by searching for clusters of cis -elements of any type chosen by the user. Cister is simple to use and is available on the web.
Availability: http://sullivan.bu.edu/~mfrith/cister.shtml
Contact: mfrith{at}bu.edu; zhiping{at}bu.edu
* To whom correspondence should be addressed.
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