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The sequencing of entire genomes is a major achievement, but the meaning of the mass of accumulated data is only just beginning to be unraveled. At first sight, the task appears straightforward: locate the genes and translate the coding regions to establish their protein products; perform similarity searches to establish relationships with previously characterized sequences and assign function by evolutionary inference; and rationalize the function in structural terms using known or model-derived structures. Given the quantity of data, the procedures should be automated as much as possible.

The reality, of course, is not so simple. Attempts to decipher the clues latent in genomic data are hampered because current methods to predict genes in uncharacterized DNA are unreliable (and it is not always clear what we mean by “gene”); it is presumptuous to make functional assignments merely on the basis of some degree …