2006, pp 246-260

Prokaryotic Genomics

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Introduction

Haemophilus influenzae strain Rd became the first free-living organism to have its genome sequenced (Fleischmann et al., 1995). The floodgates have opened with over 100 prokaryotic genomes completely or partially sequenced. However, the acquisition and analysis of sequence data is not an end in itself; instead it is a starting point for generating hypotheses that can be tested in the laboratory. It is clear that knowledge of the complete genome sequence of an organism does not tell us a great deal about the composition or functional capabilities of the organism. Homology, or sequence similarity, provides clues, but it does not prove gene function. Furthermore, a large percentage of genes have no matches to known genes. For example, at the time of sequence release, up to 62% of predicted protein-coding genes in the Methanococcus jannaschii genome had no matches with genes from other organisms (Bult et al., 1996). Elucidating the function of these “ORFan” or “FUN” ...