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Abstract:
Background: Genome sequences vary strongly in their repetitiveness and the causes for this are
still debated. Here we propose a novel measure of genome repetitiveness, the index of
repetitiveness, Ir, which can be computed in time proportional to the length of the sequences
analyzed. We apply it to 336 genomes from all three domains of life.
Results: The expected value of Ir is zero for random sequences of any G/C content and greater
than zero for sequences with excess repeats. We find that the Ir of archaea is significantly smaller
than that of eubacteria, which in turn is smaller than that of eukaryotes. Mouse chromosomes have
a significantly higher Ir than human chromosomes and within each genome the Y chromosome is
most repetitive. A sliding window analysis reveals that the human HOXA cluster and two
surrounding genes are characterized by local minima in Ir. A program for calculating the Ir is freely
available at http://adenine.biz.fh-weihenstephan.de/ir/.
Conclusion: The general measure of DNA repetitiveness proposed in this paper can be efficiently
computed on a genomic scale. This reveals a broad spectrum of repetitiveness among diverse
genomes which agrees qualitatively with previous studies of repeat content. A sliding window
analysis helps to analyze the intragenomic distribution of repeats.
