title: Comparative testing of DNA segmentation algorithms using benchmark simulations.
abstract: 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.
authors.affiliation: Department of Biology & Biochemistry, University of Houston, TX, USA. eelhaik@gmail.com
authors.forename: Eran
authors.initials: E
authors.lastname: Elhaik
authors.forename: Dan
authors.initials: D
authors.lastname: Graur
authors.forename: Kresimir
authors.initials: K
authors.lastname: Josic
mesh_terms: D000465:Algorithms; D001482:Base Composition / Q000235:genetics; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D030561:Databases, Nucleic Acid; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D013997:Time Factors
chemical_list: D004247:DNA