Bioinformatics Vol. 15 no. 12 1999
Pages 974-979
© 1999 Oxford University Press
SEGMENT: identifying compositional domains in DNA sequences
1 Department of Genetics and Institute of
Biotechnology, Faculty of Sciences, University of Granada,
E-18071-Granada, Spain
2 Department of Applied Physics, University
of Granada, Spain
3 Institute of Biotechnology, University of
Granada, E-18071-Granada, Spain
4 Department of Applied Physics II,
University of Málaga, Spain
To whom correspondence should be addressed.
Present address: Center for Polymer Studies and Department of Physics, Boston University, Massachusetts, USA.
Motivation: DNA sequences are formed by patches or domains of different nucleotide composition. In a few simple sequences, domains can simply be identified by eye; however, most DNA sequences show a complex compositional heterogeneity (fractal structure), which cannot be properly detected by current methods. Recently, a computationally efficient segmentation method to analyse such nonstationary sequence structures, based on the Jensen–Shannon entropic divergence, has been described. Specific algorithms implementing this method are now needed.
Results: Here we describe a heuristic segmentation algorithm for DNA sequences, which was implemented on a Windows program (SEGMENT). The program divides a DNA sequence into compositionally homogeneous domains by iterating a local optimization procedure at a given statistical significance. Once a sequence is partitioned into domains, a global measure of sequence compositional complexity (SCC), accounting for both the sizes and compositional biases 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 sequence complexity.
Availability: SEGMENT is available on the Web at http://www.ugr.es/local/oliver/segment/
Contact: oliver{at}ugr.es
Received on March 30, 1999
; revised on June 18, 1999
; accepted on August 4, 1999
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