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.
Current Genomics
Title:A Brief Review: The Z-curve Theory and its Application in Genome Analysis
Volume: 15 Issue: 2
Author(s): Ren Zhang and Chun-Ting Zhang
Affiliation:
Keywords: GC profile, Gene finding, Genomic island, Replication origin, Z-curve.
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.
Export Options
About this article
Cite this article as:
Zhang Ren and Zhang Chun-Ting, A Brief Review: The Z-curve Theory and its Application in Genome Analysis, Current Genomics 2014; 15 (2) . https://dx.doi.org/10.2174/1389202915999140328162433
DOI https://dx.doi.org/10.2174/1389202915999140328162433 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
Call for Papers in Thematic Issues
Advanced Computational Algorithms and Artificial Intelligence in Clinical Pharmacogenomics
In the era of personalized medicine, understanding the relationship between genetics and drug response is crucial. This issue delves into innovative methodologies, leveraging deep computational analysis and artificial intelligence, to enhance the field of Clinical Pharmacogenomics. The interdisciplinary approach harnesses the power of advanced high-throughput genotyping technologies, sophisticated computational analysis, ...read more
Applications of Single-cell Sequencing Technology in Reproductive Medicine
Single cell sequencing (SCS) technology utilizes individual cells' genetic material to sequence their genome, transcriptome, and epigenetics at the molecular level. It offers insights into cell heterogeneity and enables the study of limited biological materials. Since its recognition as a valuable technique in 2011, single cell sequencing has yielded numerous ...read more
Big Data in Cancer Research
Cancer is a significant threat to human life and health, remaining a highly aggressive killer. It is a leading cause of death worldwide and represents a crucial medical issue for humanity. However, in the past decade, the effectiveness of new synthetic anticancer agents has not matched the current clinical speculation. ...read more
Current Genomics in Cardiovascular Research
Cardiovascular diseases are the main cause of death in the world, in recent years we have had important advances in the interaction between cardiovascular disease and genomics. In this Research Topic, we intend for researchers to present their results with a focus on basic, translational and clinical investigations associated with ...read more
Related Journals
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
The Formation of 2-Isoxazolines in the Reactions of α,β-Unsaturated Carbonyl Compounds with Hydroxylamine and its Derivatives-A Critical Review
Current Organic Chemistry Current Practice and Controversies in Screening for Gestational Diabetes
Current Diabetes Reviews Carotenoids and Cardiovascular Risk
Current Pharmaceutical Design Meet Our Editorial Board Member
Current Nutrition & Food Science Mycobacterium tuberculosis-Secreted Tyrosine Phosphatases as Targets Against Tuberculosis: Exploring Natural Sources in Searching for New Drugs
Current Pharmaceutical Design Remdesivir: Mechanism of Metabolic Conversion from Prodrug to Drug
Current Drug Metabolism Monooxime Bispyridinium Reactivators Bearing Xylene Linker Synthesis and In Vitro Evaluation on Model of Organophosphate-Inhibited Acetylcholinesterase
Medicinal Chemistry Rho Kinase Inhibitors and Novel Ocular Drug Delivery Systems- A Revolutionary Step Towards the Treatment of Glaucoma
Current Drug Delivery A Ligands View of Target Similarity: Chemogenomic Binding Site- Directed Techniques for Drug Discovery
Current Topics in Medicinal Chemistry From Vancomycin to Oritavancin: The Discovery and Development of a Novel Lipoglycopeptide Antibiotic
Anti-Infective Agents in Medicinal Chemistry Role of Secretory Phospholipase A2 in CNS Inflammation: Implications in Traumatic Spinal Cord Injury
CNS & Neurological Disorders - Drug Targets Small Molecule p38 Inhibitors: Novel Structural Features and Advances from 2002-2005
Current Topics in Medicinal Chemistry Human Ascariasis: An Updated Review
Recent Patents on Inflammation & Allergy Drug Discovery Use of Total Parenteral Nutrition in Severe Anorexia Nervosa Complicated by a Gastrointestinal Illness
Current Nutrition & Food Science Design, Synthesis, Antimicrobial Evaluation and Molecular Modeling Study of New 2-mercaptoimidazoles (Series-III)
Letters in Drug Design & Discovery Withdrawal Notice: Current Drug Trends for the Treatment of the SARS- CoV-2
Coronaviruses Continuous Renal Replacement Therapy in Children Post-Hematopoietic Stem Cell Transplantation: The Present and the Future
Current Stem Cell Research & Therapy Prodigiosins as Anti Cancer Agents: Living Upto Their Name
Current Pharmaceutical Design Subject Index To Volume 2
Current Computer-Aided Drug Design Antimicrobial Activities of Various Thiazine Based Heterocyclic Compounds: A Mini-Review
Mini-Reviews in Organic Chemistry