Abstract
Predicting genes and gene regions undergoing adaptive evolution is one of the most important aims of geneticists and of new emerging areas of investigation. As more genomes are being sequenced and computational tools to detect selection are being developed, the number of genes uncovered as being positively selected is overwhelming. Several statistical methods have been devised to test if specific amino acid regions have undergone adaptive mutations at some stage during the proteins evolution. Despite the sensitivity of these methods to detect selective constraints, they are still based on linear sequence alignments and therefore, examine only one dimension of the proteins evolution. Few methods have been designed to detect intra-molecular co-evolution between amino acid sites. However, no tests are performed to determine the adaptive value of these co-evolutionary events. Conclusions independently derived from both types of methods are ambiguous and seldom unequivocal, since evolution of protein sequences is most likely to be multifactorial. This review discusses and has briefly exposed the advantages and disadvantages of the many different methods and computational tools to detect adaptive evolution and co-evolution. Further, the potential that the combination of such methods has in providing more biologically meaningful results is highlighted.
Keywords: Adaptive evolution, coevolution, statistical methods, maximum likelihood, parsimony, covarion model
Current Bioinformatics
Title: Computational and Statistical Methods to Explore the Various Dimensions of Protein Evolution
Volume: 1 Issue: 2
Author(s): Mario A. Fares
Affiliation:
Keywords: Adaptive evolution, coevolution, statistical methods, maximum likelihood, parsimony, covarion model
Abstract: Predicting genes and gene regions undergoing adaptive evolution is one of the most important aims of geneticists and of new emerging areas of investigation. As more genomes are being sequenced and computational tools to detect selection are being developed, the number of genes uncovered as being positively selected is overwhelming. Several statistical methods have been devised to test if specific amino acid regions have undergone adaptive mutations at some stage during the proteins evolution. Despite the sensitivity of these methods to detect selective constraints, they are still based on linear sequence alignments and therefore, examine only one dimension of the proteins evolution. Few methods have been designed to detect intra-molecular co-evolution between amino acid sites. However, no tests are performed to determine the adaptive value of these co-evolutionary events. Conclusions independently derived from both types of methods are ambiguous and seldom unequivocal, since evolution of protein sequences is most likely to be multifactorial. This review discusses and has briefly exposed the advantages and disadvantages of the many different methods and computational tools to detect adaptive evolution and co-evolution. Further, the potential that the combination of such methods has in providing more biologically meaningful results is highlighted.
Export Options
About this article
Cite this article as:
Fares A. Mario, Computational and Statistical Methods to Explore the Various Dimensions of Protein Evolution, Current Bioinformatics 2006; 1 (2) . https://dx.doi.org/10.2174/157489306777011950
DOI https://dx.doi.org/10.2174/157489306777011950 |
Print ISSN 1574-8936 |
Publisher Name Bentham Science Publisher |
Online ISSN 2212-392X |
- 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
Related Articles
-
Angiogenesis New Targets for the Development of Anticancer Chemotherapies
Current Pharmaceutical Design Serum Vitamin E (α-Tocopherol) Estimation: A Potential Biomarker of Antioxidant Status Evaluation on Heavy Metal Toxicities
Recent Patents on Biomarkers Antiviral Sensing in Teleost Fish
Current Pharmaceutical Design Implications of Nanoscale Based Drug Delivery Systems in Delivery and Targeting Tubulin Binding Agent, Noscapine in Cancer Cells
Current Drug Metabolism Cigarette Smoking, Metabolic Activation and Carcinogenesis
Current Drug Metabolism Optimizing Outcomes Following Allogeneic Hematopoietic Progenitor Cell Transplantation in AML: The Role of Hypomethylating Agents
Current Cancer Drug Targets Nano Drug Delivery in Treatment of Oral Cancer, A Review of the Literature
Current Drug Targets Improving the Effect of FDA-Mandated Drug Safety Alerts with Internet- Based Continuing Medical Education
Current Drug Safety Evaluation of Ocular Irritation and Bioavailability of Voriconazole Loaded Microemulsion
Current Drug Delivery Immunotherapy of Cancer Based on DC-Tumor Fusion Vaccine
Current Immunology Reviews (Discontinued) Understanding Tumor-Antigen Presentation in the New Era of Cancer Immunotherapy
Current Pharmaceutical Design Genistein: A Boon for Mitigating Ischemic Stroke
Current Topics in Medicinal Chemistry Phase II Drug Metabolism and Individualized Drug Therapy: A Focus on Functional Genetic Variation in UDP-Glucuronosyltransferases
Current Pharmacogenomics and Personalized Medicine “PARG Inhibitors’ Success: A Long Way to Go!”
Current Enzyme Inhibition A Review: The Anti-inflammatory, Anticancer and Antibacterial Properties of Four Kinds of Licorice Flavonoids Isolated from Licorice
Current Medicinal Chemistry Protein Microarrays for Studies of Drug Mechanisms and Biomarker Discovery in the Era of Systems Biology
Current Pharmaceutical Design Novel Drug Therapies for Fertility Preservation in Men Undergoing Chemotherapy: Clinical Relevance of Protector Agents
Current Medicinal Chemistry In Vitro and In Vivo Models for Analysis of Resistance to Anticancer Molecular Therapies
Current Medicinal Chemistry IAP Proteins Antagonist: An Introduction and Chemistry of Smac Mimetics under Clinical Development
Current Medicinal Chemistry Sunlight Vitamin D and Skin Cancer
Anti-Cancer Agents in Medicinal Chemistry