Why are complementary DNA strands symmetric?
Identifieur interne : 000D31 ( Istex/Checkpoint ); précédent : 000D30; suivant : 000D32Why are complementary DNA strands symmetric?
Auteurs : Pierre-Franc Ois Baisne E ; Steve Hampson ; Pierre Baldi [États-Unis]Source :
- Bioinformatics [ 1367-4803 ] ; 2002.
Abstract
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@ics.uci.edu hampson@ics.uci.edu pfbaldi@ics.uci.edu Data: http://promoter.ics.uci.edu/RevCompSym/ * To whom correspondence should be addressed.
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DOI: 10.1093/bioinformatics/18.8.1021
Affiliations:
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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@ics.uci.edu hampson@ics.uci.edu pfbaldi@ics.uci.edu Data: http://promoter.ics.uci.edu/RevCompSym/ * To whom correspondence should be addressed.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Baisne E, Pierre Franc Ois" sort="Baisne E, Pierre Franc Ois" uniqKey="Baisne E P" first="Pierre-Franc Ois" last="Baisne E">Pierre-Franc Ois Baisne E</name><name sortKey="Hampson, Steve" sort="Hampson, Steve" uniqKey="Hampson S" first="Steve" last="Hampson">Steve Hampson</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Baldi, Pierre" sort="Baldi, Pierre" uniqKey="Baldi P" first="Pierre" last="Baldi">Pierre Baldi</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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