Comparative analysis of regulatory patterns in bacterial genomes

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Abstract
Recognition of transcription regulatory sites in bacterial genomes is a notoriously difficult problem. There are no algorithms capable of making reliable predictions even for well-studied sites such as the CRP (cyclic AMP receptor protein) box. However, availability of complete bacterial genomes makes it possible to make reliable predictions with bad rules. This comparative approach is based on the assumption that sets of co-regulated genes are conserved in related bacteria. Thus true sites occur upstream of orthologous genes, whereas false candidates are scattered at random.

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