Comparative testing of DNA segmentation algorithms using benchmark simulations

Research output: Contribution to journalArticle


Numerous segmentation methods for the detection of compositionally homogeneous domains within genomic sequences have been proposed. Unfortunately, these methods yield inconsistent results. Here, 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 guanine and cytosine (GC) content variability. The sequences in the second set are composed of a mosaic of many short domains and a few long ones, distinguished by sharp GC content boundaries between neighboring domains. We use these sets to test the performance of seven segmentation algorithms in the literature. 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.


External organisations
  • University of Houston
Research areas and keywords


  • Algorithms, Base Composition/genetics, Base Pairing/genetics, Base Sequence, Chromosomes, Human, Pair 1/genetics, Computational Biology/methods, Computer Simulation, DNA/genetics, Databases, Nucleic Acid, Genome, Human/genetics, Humans, Sequence Analysis, DNA/methods, Time Factors
Original languageEnglish
Pages (from-to)1015-1024
JournalMolecular biology and evolution
Issue number5
Publication statusPublished - 2010 May
Publication categoryResearch
Externally publishedYes