Bioinformatics Vol. 18 no. 8 2002
Pages 1021-1033
© 2002 Oxford University Press
Why are complementary DNA strands symmetric?
1 Department of Information and Computer Science,
Institute for Genomics and Bioinformatics and
2 Department of Biological Chemistry, College of Medicine,
University of California, Irvine, CA 92697-3425, USA
Received on November 24, 2001
; revised on March 7, 2002
; accepted on March 11, 2002
Motivation: Over sufficiently long windows, complementary strands of DNA tend to have the same base composition. A few reports have indicated that this first-order parity rule extends at higher orders to oligonucleotide composition, at least in some organisms or taxa. However, the scientific literature falls short of providing a comprehensive study of reverse-complement symmetry at multiple orders and across the kingdom of life. It also lacks a characterization of this symmetry and a convincing explanation or clarification of its origin.
Results: We develop methods to measure and characterize symmetry at multiple orders, and analyze a wide set of genomes, encompassing single- and double-stranded RNA and DNA viruses, bacteria, archae, mitochondria, and eukaryota. We quantify symmetry at orders 1 to 9 for contiguous sequences and pools of coding and non-coding upstream regions, compare the observed symmetry levels to those predicted by simple statistical models, and factor out the effect of lower-order distributions. We establish the universality and variability range of first-order strand symmetry, as well as of its higher-order extensions, and demonstrate the existence of genuine high-order symmetric constraints. We show that ubiquitous reverse-complement symmetry does not result from a single cause, such as point mutation or recombination, but rather emerges from the combined effects of a wide spectrum of mechanisms operating at multiple orders and length scales.
Contact: baisnee{at}ics.uci.edu hampson{at}ics.uci.edu pfbaldi{at}ics.uci.edu
Data: http://promoter.ics.uci.edu/RevCompSym/
* To whom correspondence should be addressed.
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