Recurrence analysis provides a useful tool for the characterisation of oligonucleotide usage along genomic tracts. While coding regions are characterised by a low-recurrence regimen (except in the case of intragenic repeats) introns and intergenic regions exhibit a high density of recurring oligos, and appear to be correlated from the point of view of oligonucleotide preference. By comparing homologous loci in Plasmodium falciparum and P. berghei, it can be seen that introns and intergenic regions, though exhibiting very low sequence similarity, do not drift without constraints, but maintain a consistent use of the same oligos in the two species.
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