We compare and contrast genome-wide compositional biases and distributions of 
short oligonucleotides across 15 diverse prokaryotes that have substantial 
genomic sequence collections. These include seven complete genomes (Escherichia 
coli, Haemophilus influenzae, Mycoplasma genitalium, Mycoplasma pneumoniae, 
Synechocystis sp. strain PCC6803, Methanococcus jannaschii, and Pyrobaculum 
aerophilum). A key observation concerns the constancy of the dinucleotide 
relative abundance profiles over multiple 50-kb disjoint contigs within the same 
genome. (The profile is rhoXY* = fXY*/fX*fY* for all XY, where fX* denotes the 
frequency of the nucleotide X and fY* denotes the frequency of the dinucleotide 
XY, both computed from the sequence concatenated with its inverted complementary 
sequence.) On the basis of this constancy, we refer to the collection [rhoXY*] 
as the genome signature. We establish that the differences between [rhoXY*] 
vectors of 50-kb sample contigs of different genomes virtually always exceed the 
differences between those of the same genomes. Various di- and tetranucleotide 
biases are identified. In particular, we find that the dinucleotide CpG=CG is 
underrepresented in many thermophiles (e.g., M. jannaschii, Sulfolobus sp., and 
M. thermoautotrophicum) but overrepresented in halobacteria. TA is broadly 
underrepresented in prokaryotes and eukaryotes, but normal counts appear in 
Sulfolobus and P. aerophilum sequences. More than for any other bacterial 
genome, palindromic tetranucleotides are underrepresented in H. influenzae. The 
M. jannaschii sequence is unprecedented in its extreme underrepresentation of 
CTAG tetranucleotides and in the anomalous distribution of CTAG sites around the 
genome. Comparative analysis of numbers of long tetranucleotide microsatellites 
distinguishes H. influenzae. Dinucleotide relative abundance differences between 
bacterial sequences are compared. For example, in these assessments of 
differences, the cyanobacteria Synechocystis, Synechococcus, and Anabaena do not 
form a coherent group and are as far from each other as general gram-negative 
sequences are from general gram-positive sequences. The difference of M. 
jannaschii from low-G+C gram-positive proteobacteria is one-half of the 
difference from gram-negative proteobacteria. Interpretations and hypotheses 
center on the role of the genome signature in highlighting similarities and 
dissimilarities across different classes of prokaryotic species, possible 
mechanisms underlying the genome signature, the form and level of genome 
compositional flux, the use of the genome signature as a chronometer of 
molecular phylogeny, and implications with respect to the three putative 
eubacterial, archaeal, and eukaryote domains of life and to the origin and early 
evolution of eukaryotes.