With the completion of more than 24 prokaryotic genome sequences and many more currently in progress, the major task of identifying the functions of all genes in these organisms is still many years ahead. In fact, even the first step of mapping all the genes in the final version of these genomes is still a major problem. The identification of protein coding regions in genomic sequences can until now only be accomplished by combining powerful computational tools with work intensive experimental approaches. The advancements of bioinformatics in the context of genomes have been overwhelming but the basic analysis of predicting coding and non-coding locations and the precise boundaries of their transcripts are still performed with great uncertainties. The prediction of promoter locations is also difficult. An E.coli high density oligonucleotide array has been synthesized and contains all the annotated coding (open-reading-frames) and non-coding (intergenic) regions. One use of this array is to provide a new tool to assist in identifying RNA transcripts expressed under defined conditions. The information retrieved from the high-density oligonucleotide array was used to characterize gene expression and to identify previously unidentified RNA transcripts. This analyzes led to the identification of new operons, promoter regions, regulatory regions and previously unidentified transcripts within the non-coding regions of the E.coli genome.
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