SEGMENT: identifying compositional domains in DNA sequences

Motivation: DNA sequences are formed by patches or domains of different nuc leotide composition. In a few simple sequences, domains can simply be ident ified by eye; however; most DNA sequences show a complex compositional hete rogeneity (fractal structure), which cannot be properly detected by current methods. Recently, a computationally efficient segmentation method to anal yse such nonstationary sequence structures, based on the Jensen-Shannon ent ropic divergence, has been described. Specific algorithms implementing this method are now needed. Results: Here we describe a heuristic segmentation algorithm for DNA sequen ces, which was implemented an a Windows program (SEGMENT). The program divi des a DNA sequence into compositionally homogeneous domains by iterating a local optimization procedure at a given statistical significance. Once a se quence is partitioned into domains, a global measure of sequence compositio nal complexity (SCC), accounting for both the sizes and compositional biase s of all the domains in the sequence, is derived. SEGMENT computes SCC as a function of the significance level, which provides a multiscale view of se quence complexity.