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Comparative testing of DNA segmentation algorithms using benchmark
simulations
E. Elhaik, D. Graur and K. Josić
Numerous segmentation
methods for the detection of compositionally homogeneous
domains within genomic sequences have been proposed. Unfortunately,
these
methods yield inconsistent results. To address this problem we present
a benchmark
consisting of two sets of simulated genomic sequences for testing the
performances of
segmentation algorithms. Sequences in the first set are composed of
fixed-sized
homogeneous domains, distinct in their between-domain GC content
variability. The
chromosomal sequences in the second set are composed of a mosaic of
many short
domains and few long domains distinguished by sharp GC content
boundaries
between neighboring ones. We use these benchmarks to test the
performance of seven
previously proposed. Our results show that recursive segmentation
algorithms based
on the Jensen-Shannon divergence outperform all other algorithms.
However, even
these algorithms perform poorly in certain instances because of the
arbitrary choice of
a segmentation stopping criterion
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