Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm.

ABSTRACT: It has been suggested that the mammalian genome is composed mainly of long compositionally homogeneous domains. Such domains are frequently identified using recursive segmentation algorithms based on the Jensen-Shannon divergence. However, a common difficulty with such methods is deciding when to halt the recursive partitioning and what criteria to use in deciding whether a detected boundary between two segments is real or not. We demonstrate that commonly used halting criteria are intrinsically biased, and propose IsoPlotter, a parameter-free segmentation algorithm that overcomes such biases by using a simple dynamic halting criterion and tests the homogeneity of the inferred domains. IsoPlotter was compared with an alternative segmentation algorithm, D(JS), using two sets of simulated ge

SUBMITTER: Elhaik E 

PROVIDER: S-EPMC2926622 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature