Predicting bacterial transcription units using sequence and expression data | Zendy

Joseph Bockhorst | Zendy; Yu Qiu | Zendy; Jeremy D. Glasner | Zendy; Mingzhu Liu | Zendy; Frederick R. Blattner | Zendy; Mark Craven | Zendy

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Predicting bacterial transcription units using sequence and expression data

Author(s) -

Joseph Bockhorst,

Yu Qiu,

Jeremy D. Glasner,

Mingzhu Liu,

Frederick R. Blattner,

Mark Craven

Publication year - 2003

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btg1003

Subject(s) - promoter , operon , computational biology , genome , transcription (linguistics) , gene , probabilistic logic , biology , sequence (biology) , genetics , dna sequencing , gene expression , computer science , escherichia coli , artificial intelligence , linguistics , philosophy

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.

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