A Brief Review: The Z-curve Theory and its Application in Genome Analysis

ISSN: 1875-5488 (Online)
ISSN: 1389-2029 (Print)


Volume 15, 6 Issues, 2014


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Current Genomics

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Christian Néri
Institute of Biology Paris-Seine
CNRS UMR 8256 and UPMC
Paris, 75005
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A Brief Review: The Z-curve Theory and its Application in Genome Analysis

Author(s): Ren Zhang and Chun-Ting Zhang

Affiliation: Center for Molecular Medicine and Genetics, Wayne State University Medical School, Detroit, MI 48201, USA.

Abstract

In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.

Keywords: GC profile, Gene finding, Genomic island, Replication origin, Z-curve.

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Article Details

Volume: 15
Issue Number: 2
First Page: 78
Last Page: 94
Page Count: 17
DOI: 10.2174/1389202915999140328162433
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