June 17, 2021

Download Ebook Free Multivariate Analyses Of Codon Usage Biases

Multivariate Analyses of Codon Usage Biases

Multivariate Analyses of Codon Usage Biases
Author : Jean R. Lobry
Publisher : Elsevier
Release Date : 2018-11-20
Category : Computers
Total pages :168
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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
Author : Amanda L. Hanes
Publisher : Unknown
Release Date : 2009
Category : Nucleotides
Total pages :106
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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.

Genetics Abstracts

Genetics Abstracts
Author : Anonim
Publisher : Unknown
Release Date : 1998
Category : Genetics
Total pages :129
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Zoological Studies

Zoological Studies
Author : Anonim
Publisher : Unknown
Release Date : 2007
Category : Animals
Total pages :129
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Proceedings of the 4th Asia-Pacific Bioinformatics Conference

Proceedings of the 4th Asia-Pacific Bioinformatics Conference
Author : Tao Jiang,Ueng-Cheng Yang,Yi-Ping Phoebe Chen,Limsoon Wong
Publisher : World Scientific
Release Date : 2005-12-13
Category : Computers
Total pages :380
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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

Genome Research

Genome Research
Author : Anonim
Publisher : Unknown
Release Date : 2009
Category : DNA polymerases
Total pages :129
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Can J Microbiol

Can J Microbiol
Author : Anonim
Publisher : Unknown
Release Date : 2011
Category : Microbiology
Total pages :129
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Quantitative Aspects of Gene Expression

Quantitative Aspects of Gene Expression
Author : Jiong Ma
Publisher : Unknown
Release Date : 2006
Category :
Total pages :444
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Plant Breeding Abstracts

Plant Breeding Abstracts
Author : Anonim
Publisher : Unknown
Release Date : 1999
Category : Plant breeding
Total pages :129
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Computing and Combinatorics

Computing and Combinatorics
Author : Anonim
Publisher : Unknown
Release Date : 2005
Category : Combinatorial analysis
Total pages :129
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Annual Report

Annual Report
Author : Scottish Crop Research Institute
Publisher : Unknown
Release Date : 1998
Category : Horticultural research
Total pages :129
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Proceedings of the 4th Asia-Pacific Bioinformatics Conference

Proceedings of the 4th Asia-Pacific Bioinformatics Conference
Author : Tao Jiang,Limsoon Wong,Ueng-Cheng Yang,Yi-Ping Phoebe Chen
Publisher : Series on Advances in Bioinfor
Release Date : 2006
Category : Computers
Total pages :363
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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.

Tsinghua Science and Technology

Tsinghua Science and Technology
Author : Anonim
Publisher : Unknown
Release Date : 2004
Category : Science
Total pages :129
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Journal of the Inland Fisheries Society of India

Journal of the Inland Fisheries Society of India
Author : Inland Fisheries Society of India
Publisher : Unknown
Release Date : 2008
Category : Fish-culture
Total pages :129
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