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Bioinformatics Vol. 18 no. 90001 2002
Pages S337-S344
© 2002 Oxford University Press

Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis

Brian Tjaden 1,*, David R. Haynor 2, Sergey Stolyar 3, Carsten Rosenow 4 and Eugene Kolker 3

1 Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
2 Department of Radiology, University of Washington, University of Washington, Box 356004, Seattle, WA 98195, USA
4 Institute for Systems Biology, 1441 North 34th St., Seattle, WA 98103, USA
4 Affymetrix Inc., 3380 Central Expressway, Santa Clara, CA 95051, USA

Received on January 22, 2002 ; revised on March 29, 2002 ; accepted on March 29, 2002

Microarrays traditionally have been used to assay the transcript expression of coding regions of genes. Here, we use Escherichia coli oligonucleotide microarrays to assay transcript expression of both open reading frames (ORFs) and intergenic regions. We then use hidden Markov models to analyse this expression data and estimate transcription boundaries of genes. This approach allows us to identify 5' untranslated regions (5' UTRs) of transcripts as well as genes that are likely to be operon members. The operon elements we identify correspond to documented operons with 99% specificity and 63% sensitivity. Similarly we find that our 5' UTR results accurately coincide with experimentally verified promoter regions for most genes.

Contact: tjaden{at}cs.washington.edu

Keywords: untranslated regions; operons; intergenic; microarrays; Escherichia coli.

* To whom correspondence should be addressed.


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