From function to sequence, an integrated view of the genome texts

The Darwinian triplet variation/selection/amplification made material systems evolve. Evolution created functions, that captured structures to be actualised. Finally, the blueprints for structures were imbedded into DNA sequences. The time course and orientation of this process has an important consequence. With the sequence (or even the structure) alone, it is impossible to tell the function of a gene. Approaches allowing integration of biological knowledge with genome texts are reviewed, with emphasis on the concept of neigbourhood, illustrated in the case of codon preference in genes.