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Multivariate Analyses Of Codon Usage Biases

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Multivariate Analyses of Codon Usage Biases

Multivariate Analyses of Codon Usage Biases Book
Author : Jean R. Lobry
Publisher : Elsevier
Release : 2018-11-20
ISBN : 0128172517
Language : En, Es, Fr & De

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Book Description :

A complete case study with all coding sequences from the bacteria Borrellia burgdorferi illustrates how multivariate analyses reveals evolutionary mechanisms acting at the molecular level. They are either mutationnal (symmetric and asymmetric directionnal mutation pressure) or selective (selection against head-on collisions or linked to gene expressivity or subcellular location). The main objective is to provide a complete and reproducible example of the power of multivariate analyses in this application field

Investigation and Quantification of Codon Usage Bias Trends in Prokaryotes

Investigation and Quantification of Codon Usage Bias Trends in Prokaryotes Book
Author : Amanda L. Hanes
Publisher : Unknown
Release : 2009
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Organisms construct proteins out of individual amino acids using instructions encoded in the nucleotide sequence of a DNA molecule. The genetic code associates combinations of three nucleotides, called codons, with every amino acid. Most amino acids are associated with multiple synonymous codons, but although they result in the same amino acid and thus have no effect on the final protein, synonymous codons are not present in equal amounts in the genomes of most organisms. This phenomenon is known as codon usage bias, and the literature has shown that all organisms display a unique pattern of codon usage. Research also suggests that organisms with similar codon usage share biological similarities as well. This thesis helps to verify this theory by using an existing computational algorithm along with multivariate analysis to demonstrate that there is a significant difference between the codon usage of free-living prokaryotes and that of obligate intracellular prokaryotes. The observed difference is primarily the result of GC content, with the additional effect of an unknown factor. Although the existing literature often mentions the strength of biased codon usage, it does not contain a clear, consistent definition of the concept. This thesis provides a disambiguated definition of bias strength and clarifies the relationships between this and other properties of biased codon usage. A bias strength metric, designed to match the given definition of bias strength, is proposed. Evaluation of this metric demonstrates that it compares favorably with existing metrics used in the literature as criteria for bias strength, and also suggests that codon usage bias in general follows the trend of being either strong and global to the genome, or weak and present in only a subset of the genome. Analysis of these metrics provides insight into the unknown factor partially responsible for the codon usage difference between free-living and obligatorily intracellular prokaryotes, and the proposed bias strength metric is used to draw conclusions about the characteristics of GC-content bias.

Proceedings of the 4th Asia Pacific Bioinformatics Conference

Proceedings of the 4th Asia Pacific Bioinformatics Conference Book
Author : Tao Jiang,Ueng-Cheng Yang,Yi-Ping Phoebe Chen,Limsoon Wong
Publisher : World Scientific
Release : 2005-12-13
ISBN : 1783260033
Language : En, Es, Fr & De

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Book Description :

High-throughput sequencing and functional genomics technologies have given us a draft human genome sequence and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, and gene expression profiles of normal and diseased tissues in different clinical states are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the annotation of genomic sequences, in the understanding of the interplay between genes and proteins, in the analysis of the genetic variability of species, and so on. This proceedings contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics, by researchers, professionals, and industrial practitioners at the 4th Asia-Pacific Bioinformatics Conference held in Taipei in February 2006. Contents:Accuracy of Four Heuristics for the Full Sibship Reconstruction Problem in the Presence of Genotype Errors (D A Konovalov)Predicting Ranked SCOP Domains by Mining Asociations of Visual Contents in Distance Matrices (P-H Chi & C-R Shyu)An Efficient Algorithm for String Motif Discovery (F Y L Chin & H C M Leung)On the Complexity of Finding Control Strategies for Boolean Networks (T Akutsu et al.)Microarray Missing Value Imputation by Iterated Local Least Squares (Z Cai et al.)Techniques for Assessing Phylogenetic Branch Support: A Performance Study (D Ruths & L Nakhleh)Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes (S-S Huang et al.)A Knowledge-Based Approach to Protein Local Structure Prediction (C-T Chen et al.)Resolving the Gene Tree and Species Tree Problem by Phylogenetic Mining (X Han)Gene Expression Data Clustering Based on Local Similarity Combination (D Pan & F Wang)and other papers Readership: Academics, researchers, graduate students in bioinformatics and computer science. Keywords:Bioinformatics;Computational Biology;Systems Biology;Statistical Modeling;Comparative Genomics;Evolutionary Biology;Data Mining;Structural Bioinformatics;Statistical Genetics

The COVID 19 Pandemic Epidemiology Molecular Biology and Therapy

The COVID 19 Pandemic  Epidemiology  Molecular Biology and Therapy Book
Author : Shama Parveen
Publisher : Bentham Science Publishers
Release : 2021-02-01
ISBN : 9811481857
Language : En, Es, Fr & De

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Book Description :

The Coronavirus Disease 2019 (COVID-19) pandemic has affected almost every part of the globe with millions of cases and over a million deaths. The pandemic has had a significant global economic impact and addressing it systematically requires significant efforts from researchers, healthcare workers and governments. The COVID-19 Pandemic covers relevant aspects of this viral pandemic including information about the SARS-CoV-2 pathogen (morphology, genome, proteins, structural protein genes, replication), global epidemiology, transmission, risk factors, clinical manifestation, management, host immune response, pathogenesis, diagnosis and therapeutic agents (antivirals, natural compounds and vaccines). Readers will find basic and advanced knowledge about the disease organized into simple and easy-to-read chapters about the disease, making this book a handy and comprehensive reference for general readers, academics and biology students, alike.

Codon Evolution

Codon Evolution Book
Author : Gina M. Cannarozzi,Adrian Schneider
Publisher : Oxford University Press
Release : 2012-02-23
ISBN : 019960116X
Language : En, Es, Fr & De

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Book Description :

The second part of the book focuses on codon usage bias.

Evolutionary Biology Exobiology and Evolutionary Mechanisms

Evolutionary Biology  Exobiology and Evolutionary Mechanisms Book
Author : Pierre Pontarotti
Publisher : Springer Science & Business Media
Release : 2013-07-03
ISBN : 3642382126
Language : En, Es, Fr & De

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Book Description :

This book presents 19 selected contributions to the 16th Evolutionary Biology Meeting, which took place in September 2012 in Marseilles. The aims of these annual meetings, which gather together leading evolutionary biologists and other scientists, are to promote the exchange of ideas and to encourage interdisciplinary collaborations. The first chapter deals with the history of a great discovery: The first experiments on ascidian and sea urchin egg fertilization. The remaining contributions are grouped under the following categories: · Evolutionary biology concepts · Exobiology and the origin of life · Evolutionary mechanisms Offering an up-to-date overview of recent findings in the field of evolutionary biology, this book is an invaluable source of information for scientists, teachers and advanced students.

Information Technology and Agricultural Engineering

Information Technology and Agricultural Engineering Book
Author : Egui Zhu,Sabo Sambath
Publisher : Springer Science & Business Media
Release : 2012-02-02
ISBN : 3642275370
Language : En, Es, Fr & De

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Book Description :

This volume comprises the papers from 2011 International Conference on Information Technology and Agricultural Engineering (ICITAE 2011). 2011 International Conference on Information Technology and Agricultural Engineering (ICITAE 2011) has been held in Sanya, China, December 1-2, 2011. All the papers have been peer reviewed by the selected experts. These papers represent the latest development in the field of materials manufacturing technology, spanning from the fundamentals to new technologies and applications. Specially, these papers cover the topics of Information Technology and Agricultural Engineering. This book provides a greatly valuable reference for researchers in the field of Information Technology and Agricultural Engineering who wish to further understand the underlying mechanisms and create innovative and practical techniques, systems and processes. It should also be particularly useful for engineers in information technology and agriculture who are responsible for the efficient and effective operations.

Pattern Recognition in Bioinformatics

Pattern Recognition in Bioinformatics Book
Author : Visakan Kadirkamanathan,Guido Sanguinetti,Mark Girolami,Mahesan Niranjan,Josselin Noirel
Publisher : Springer Science & Business Media
Release : 2009-08-28
ISBN : 3642040306
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the Fourth International Workshop on Pattern Recognition in Bioinformatics, PRIB 2009, held in Sheffield, UK, in September 2009. The 38 revised full papers presented were carefully reviewed and selected from numerous submissions. The topics covered by these papers range from image analysis for biomedical data to systems biology. The conference aims at crating a focus for the development and application of pattern recognition techniques in the biological domain.

Probe

Probe Book
Author : Anonim
Publisher : Unknown
Release : 1991
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Probe book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

An Atlas of Drosophila Genes

An Atlas of Drosophila Genes Book
Author : Gustavo Maroni
Publisher : Oxford University Press
Release : 1993-06-24
ISBN : 9780198023524
Language : En, Es, Fr & De

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Book Description :

Drosophila, the common fruit fly, is the most extensively studied of all organisms from the standpoint of genetics and cytology. This atlas summarizes what is known about the approximately 100 Drosophila genes for which the complete nucleotide sequence is known. Each entry includes a description of the gene's molecular organization and expression, the complete nucleotide and amino acid sequences, maps of interesting structures, highlights of functional features and promoter regulatory regions, and selected references to the primary literature. A separate section of the atlas considers different aspects of gene organization as they occur in the Drosophila genome. Topics covered include size correlations among various genetic elements, splicing signals, translation initiation signals, and codon bias. The work represents a new milestone in summarizing current information and making it easily accessible to geneticists and biologists.

Computational Methods in Systems Biology

Computational Methods in Systems Biology Book
Author : Vincent Danos,Vincent Schachter
Publisher : Springer
Release : 2005-04-01
ISBN : 3540259740
Language : En, Es, Fr & De

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Book Description :

The Computational Methods in Systems Biology (CMSB) workshop series was established in 2003 by Corrado Priami. The purpose of the workshop series is to help catalyze the convergence between computer scientists interested in language design, concurrency theory, software engineering or program verification, and physicists, mathematicians and biologists interested in the systems-level understanding of cellular processes. Systems biology was perceived as being increasingly in search of sophisticated modeling frameworks whether for representing and processing syst- level dynamics or for model analysis, comparison and refinement. One has here a clear-cut case of a must-explore field of application for the formal methods developed in computer science in the last decade. This proceedings consists of papers from the CMSB 2003 workshop. A good third of the 24 papers published here have a distinct formal methods origin; we take this as a confirmation that a synergy is building that will help solidify CMSB as a forum for cross-community exchange, thereby opening new theoretical avenues and making the field less of a potential application and more of a real one. Publication in Springer's new Lecture Notes in Bioinformatics (LNBI) offers particular visibility and impact, which we gratefully acknowledge. Our keynote speakers, Alfonso Valencia and Trey Ideker, gave challenging and somewhat humbling lectures: they made it clear that strong applications to systems biology are still some way ahead. We thank them all the more for accepting the invitation to speak and for the clarity and excitement they brought to the conference.

XIII Conference Root and Butt Rot of Forest Trees IUFRO Working Party 7 02 01

XIII Conference  Root and Butt Rot of Forest Trees  IUFRO Working Party 7 02 01 Book
Author : Paolo Capretti,C. Comparini,M. Garbelotto
Publisher : Firenze University Press
Release : 2013
ISBN : 8866553522
Language : En, Es, Fr & De

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Book Description :

Download XIII Conference Root and Butt Rot of Forest Trees IUFRO Working Party 7 02 01 book written by Paolo Capretti,C. Comparini,M. Garbelotto, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Maize

Maize Book
Author : Y. P. S. Bajaj
Publisher : Springer Science & Business Media
Release : 2012-12-06
ISBN : 364257968X
Language : En, Es, Fr & De

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Book Description :

Forty chapters deal with various aspects of tissue culture, in vitro manipulation, and other biotechnological approaches to the improvement of maize. They are arranged in eight sections: - In Vitro Technology, Callus Cultures and Regeneration of Plants, Somatic Embryogenesis. - Wide Hybridization, Embryo, Ovule, and Inflorescence Culture, in Vitro Fertilization. - Production of Haploids and Double Haploids, Anther and Pollen Culture. - Protoplast Culture, Genetic Transformation. - Somaclonal Variation and Mutations. - Molecular Biology and Physiological Studies. - Proteins and Nutritional Improvement. Pollen Storage, Cryopreservation of Germplasm.

Synthetic Biology Part B

Synthetic Biology  Part B Book
Author : Chris Voigt
Publisher : Academic Press
Release : 2011-07-15
ISBN : 0123851211
Language : En, Es, Fr & De

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Book Description :

Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. This Volume of Methods in Enzymology has been split into 2 Parts and covers topics such as Measuring and Engineering Central Dogma Processes, Mathematical and Computational Methods and Next-Generation DNA Assembly and Manipulation. Encompasses a variety of different approaches, methodologies and disciplines Split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation

RNA Biology of Microorganisms

RNA Biology of Microorganisms Book
Author : Omar Orellana,Orna Amster-Choder,Jiqiang Ling,Rajat Banerjee
Publisher : Frontiers Media SA
Release : 2021-12-31
ISBN : 2889719189
Language : En, Es, Fr & De

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Book Description :

Download RNA Biology of Microorganisms book written by Omar Orellana,Orna Amster-Choder,Jiqiang Ling,Rajat Banerjee, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Introduction to Evolutionary Genomics

Introduction to Evolutionary Genomics Book
Author : Naruya Saitou
Publisher : Springer
Release : 2018-10-25
ISBN : 331992642X
Language : En, Es, Fr & De

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Book Description :

This authoritative textbook/reference presents a comprehensive introduction to the field of evolutionary genomics. The opening chapters describe the fundamental concepts in molecular biology and genome evolution for readers without any prior background in this area. This is followed by a detailed examination of genome evolution in various different groups of organisms. The text then concludes with a review of practical methods essential to researchers in the field. This updated and revised new edition also features historical perspectives on contributions to evolutionary genomics from related fields such as molecular evolution, genetics, and numerical taxonomy. Topics and features: introduces the basics of molecular biology, covering protein structure and diversity, as well as DNA replication, transcription, and translation; examines the phylogenetic relationships of DNA sequences, and the processes of mutation, neutral evolution, and natural selection; presents a brief evolutionary history of life, surveying the key features of the genomes of prokaryotes, eukaryotes, viruses and phages, vertebrates, and humans; reviews the various biological “omic” databases, and discusses the analysis of homologous nucleotide and amino acid sequences; provides an overview of the experimental sequencing of genomes and transcriptomes, and the construction of phylogenetic trees; describes methods for estimating of evolutionary distances, and performing studies of population genetics; supplies additional supporting material at an associated website. Serving as an indispensable textbook for graduate and advanced undergraduate courses on evolutionary genomics, this accessible overview will also prove invaluable to researchers from both computer science and the biological sciences seeking a primer on the field.

Handbook of Comparative Genomics

Handbook of Comparative Genomics Book
Author : Cecilia Saccone,Graziano Pesole
Publisher : John Wiley & Sons
Release : 2005-03-11
ISBN : 0471326410
Language : En, Es, Fr & De

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Book Description :

This comprehensive reference covers the comparative methodologyinvolved in studying molecular evolution. Providing a practicalintroduction to the role of bioinformatics in comparative genomics,this publication further discusses the basic technology used ingenome sequencing projects and provides an overview of genomestorage databases currently in use. This timely and cutting-edge text also: Reviews the basic principles of genomics and gene expressionanalysis Discusses analytic methods in proteomics andtranscriptomics Includes a comprehensive list of Web resource

Proceedings of the 4th Asia Pacific Bioinformatics Conference

Proceedings of the 4th Asia Pacific Bioinformatics Conference Book
Author : Tao Jiang,Ueng-Cheng Yang,Limsoon Wong
Publisher : Advances in Bioinformatics and
Release : 2006
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

High-throughput sequencing and functional genomics technologies have given us a draft human genome sequence and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, and gene expression profiles of normal and diseased tissues in different clinical states are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the annotation of genomic sequences, in the understanding of the interplay between genes and proteins, in the analysis of the genetic variability of species, and so on. This proceedings contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics, by researchers, professionals, and industrial practitioners at the 4th Asia-Pacific Bioinformatics Conference held in Taipei in February 2006.

Transfer RNA in Protein Synthesis

Transfer RNA in Protein Synthesis Book
Author : Dolph L. Hatfield
Publisher : CRC Press
Release : 2018-01-10
ISBN : 1351094297
Language : En, Es, Fr & De

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Book Description :

Transfer RNA in Protein Synthesis is a comprehensive volume focusing on important aspects of codon usage, selection, and discrimination in the genetic code. The many different functions of tRNA and the specialized roles of the corresponding codewords in protein synthesis from initiation through termination are thoroughly discussed. Variations that occur in the initiation process, in reading the genetic code, and in the selection of codons are discussed in detail. The book also examines the role of modified nucleosides in tRNA interactions, tRNA discrimination in aminoacylation, codon discrimination in translation, and selective use of termination codons. Other topics covered include the adaptation of the tRNA population to codon usage in cells and cellular organelles, the occurence of UGA as a codon for selenocysteine in the universal genetic code, new insights into translational context effects and in codon bias, and the molecular biology of tRNA in retroviruses. The contributions of outstanding molecular biologists engaged in tRNA research and prominent investigators from other scientific disciplines, specifically retroviral research, make Transfer RNA in Protein Synthesis an essential reference work for microbiologists, biochemists, molecular biologists, geneticists, and other researchers involved in protein synthesis research.