Computer Analysis of Genetic Macromolecules : Structure, Function and Evolution

by Kolchanov, Nikolay A.; Lim, Hwa A.

• ISBN13: 9789810213787
• ISBN10: 9810213786
• Format: Hardcover
• Copyright: 1994-07-01
• Publisher: WORLD SCIENTIFIC PUB CO INC

Summary

Includes all main problems of computational molecular biology and genetics, analysis of structural and functional organization of nucleotide sequences, mechanisms of mutagenesis, investigations of mobile genetic elements and transposable sequences.

Table of Contents

Computer Analysis of Structural-functional Organization of Nucleotide Sequences	p. 1
Introduction	p. 1
A General Characterization of the Pro- and Eukaryotic Genomes	p. 1
Basic Principles of Organization of Regulatory Regions of the Eukaryotic Genome	p. 7
Generation of Genotypical Variability in the Pro- and Eukaryotic Genomes	p. 13
Computer Analysis of Functional Sites in Nucleotide Sequences	p. 15
Search for Functional Sites Using Consensus	p. 16
Use of the Classification Approach in the Construction of Consensuses (Human Splice Sites as Example)	p. 21
Analysis of Functional Sites Based on Perceptron Function (Glucocorticoid-Receptor Complexes Binding Sites as Example)	p. 28
System "Site-Video". Recognition of Functional Sites Using Recursive Context Systems	p. 35
Investigation of Human Splice Sites by the "Site-Video" System	p. 66
Analysis of Facultative Contextual Features of Site Function	p. 82
Role of Tandem Overlapping Repeats (TOR) in Site Function (Prokaryotic Promoters as Example)	p. 95
Role of Repeats in Functional Site Evolution (Attenuators as Example)	p. 102
Contextual Analysis of the Genes Encoding Proteins	p. 107
Method for Revealing Imperfect Repeats in Nucleotide Sequences	p. 107
Convergent Origin of Repeats in the Genes Encoding Globular Proteins. Analysis of Factors Determining the Presence of Direct Repeats	p. 112
Convergent Origin of Repeats in the Genes Encoding Globular Proteins. Simulation of the Convergent Origin of Direct Repeats	p. 124
Convergent Origin of Repeats in the Genes Encoding Globular Proteins. Analysis of Factors Determining the Presence of Inverted and Symmetrical Repeats	p. 129
Computer Analysis and Recognition of Exon-Intron Structure of Eukayotic Genes	p. 135
Evolutionary Causes and Scripts of Mosaic Gene Structure Origin in Eukaryotes	p. 135
Computer System GenView for Recognition for Exon-Intron Structure of Genes in the Human Genome	p. 142
Computer Analysis of mRNA Secondary Structure
RNA Secondary Structure Investigation by Contextual Analysis	p. 154
Computer Simulation of mRNA Secondary Structure and Translation Process	p. 156
Mobile Genetic Elements and Transposable Sequences: Principles of Structural-Functional Organization and Evolution	p. 167
General Characterization of Mobile Genetic Elements and Transposable Sequences in Eukaryotic Genomes	p. 167
Contextual Analysis of Dispersed Repeats in the Eukaryotic Genomes	p. 171
Enhancer-Like Structures in Dispersed Repeats	p. 171
tRNA as a Possible Primer for the Initiation of Dispersed Repeats Alu, B1, B2 and L1 Reverse Transcription	p. 175
Computer Analysis of Alu Repeats Evolution	p. 181
Phylogenetic Analysis of Alu Repeats	p. 181
Evolutionary Dynamics of the Number of Alu Repeats in the Human Genome	p. 186
Computer Simulation of Alu Repeat Evolution	p. 192
Analysis of the Distribution of Transposable Sequences Throughout the Genome	p. 197
Distribution of Alu Repeats in the Genome: Cluster Formation and Specificities of Insertion Sites	p. 197
Estimation of Alu Repeat Transposition Constants from Phylogenetical Analysis	p. 205
Investigation of Transpositional Memory Characteristics	p. 210
Exchange Processes Involving Alu Repeats	p. 214
General Estimations of Exchange Processes	p. 214
Estimation of Unequal Crossing-Over Frequency of Transposable Sequences Based on the Distribution of Flanking Repeats	p. 219
Investigation of Block Conversion in Alu Repeat Clusters	p. 225
Effects of Transpositions of Mobile Genetic Elements on Fitness	p. 231
Simulation of Alu Repeats Distribution and Their Effects on Fitness	p. 231
Activation of Mobile Genetic Element Transcription Under Heat-Shock	p. 234
Evolutionary Significance of Availability of Regulatory Sites in Mobile Genetic Elements Responding to the Environmental Changes	p. 240
Conclusion	p. 248
Computer Investigation of Molecular Mechanisms of Mutagenesis	p. 252
Role of Polynucleotide Context in Mutation and Recombination	p. 252
Mechanisms of Single and Multiple Substitutions	p. 253
Relationship of Deletions and Insertions with Repeats	p. 260
Theoretical Analysis of Mutations	p. 264
Computer System for Analysis of Molecular Mechanisms of Mutagenesis	p. 265
Database of Mutational Spectra	p. 265
Program Package	p. 265
Contribution of Nucleotide Context to Spontaneous and Induced Mutations	p. 278
Simulation of Short Heteroduplex Repair for Spontaneous Mutations	p. 278
Substitutions Caused by DNA-polymerase Errors	p. 280
Analysis of the Dislocation Model	p. 285
Nucleotide Context Accounts for Induced Mutations	p. 287
Somatic Mutations in the Immunoglobulin Genes	p. 289
Somatic Hypermutagenesis in the Immunoglobulin Genes (General Description)	p. 289
Molecular Mechanisms Responsible for Somatic Mutagenesis	p. 290
Clonal Selection of Somatic Mutations	p. 298
Deletions and Duplication Generated by Direct Repeats	p. 300
Correlation of Deletions with Direct Repeats in the Prokaryotic Genes	p. 300
Simulation of Deletions Generated by Direct Repeats	p. 305
Simulating Duplications Produced by Direct Repeats	p. 311
Structural Instability of the Prokaryotic Genome with Respect to Repeats	p. 314
Deletions and Duplications as Factors of Prokaryotic Genome Evolution	p. 317
Simulation of Evolutionary Time Course of Repeats Changes in the Prokaryotic Genome	p. 317
Instability with Respect to Repeats and Scripts of Primitive Genomic Evolution	p. 325
Investigation of Protein Structural-Functional Organization and Evolution	p. 336
Principles of Protein Structural-Functional Organization and Evolution	p. 336
Architectonics of the Protein Molecule	p. 336
Mutations, Protein Structure and Function	p. 344
Scenarios of Protein Molecular Evolution	p. 346
Computer Analysis of Globular Proteins Secondary Structure	p. 352
Secondary Structure Prediction Based on the Discriminant Analysis	p. 352
Mutation Effects on the Secondary Structure of Globular Proteins	p. 364
Computer Analysis of Mutation Effects on [alpha]-Helical Protein Folding	p. 367
A Simple Method for Calculation of Low Energy Packaging of the [alpha]-Helices in Globular Proteins	p. 367
Effects of Amino Acid Substitutions on the Packaging of the [alpha]-Helices in Globins	p. 374
Effects of Deletions and Insertions on the Packaging of the [alpha]-Helices	p. 379
Analysis of Proteins Structure and Evolution Using the Topological Approach	p. 384
Topological Description of the [alpha]/[beta]-Domains of Globular Proteins	p. 384
Expert Rules Specifying the Number of Topologically Permissible Variants of the [alpha]/[beta]-Domains of Globular Proteins	p. 392
Method for Prediction of the Topological Structure [alpha]/[beta]-Domains	p. 402
Prediction of the [alpha]/[beta]-Domain Topologies of Proteins Based on Their Primary and Secondary Structures	p. 404
Mutational Spectrum Analysis via Simulation of Protein Topological Structure	p. 410
Conformational Stability and Evolution of Proteins	p. 418
Method for Estimating Protein Stability Alteration Resulting from Amino Acid Substitutions	p. 418
Analysis of Amino Acid Substitutions Leading to Instability in the Human Hemoglobin	p. 432
Investigation of Properties of Mutation Spectra Determined by Protein Structure Stability	p. 435
Computer Analysis of Proteins Using the Structural-Functional Determinant Approach	p. 439
Method for Recognition of Structural-Functional Determinants of Protein Molecules	p. 439
Classification of Proteins Interacting with DNA(RNA) Based on the Recognition of Structural-Functional Determinants	p. 451
Reconstruction of the Structural-Functional Organization of the N-end Domain of Histone H4 According to Its Amino Acid Sequence	p. 460
Structural-Functional Relationship in Bacterial RecA Protein: Computer Analysis of the Primary Structure of RecA Protein Family	p. 469
Genetic Macromolecules: Principles and Mechanisms of Evolution	p. 478
Problem of Neutrality and Adaptivity of Molecular Evolution	p. 478
Computer System for the Analysis of Molecular Evolution	p. 481
The Method for Multiple Alignment of Nucleotide Sequences and Compilation of Homologous Genes Database	p. 481
Reconstruction of Phylogenetic Trees	p. 489
Computer Simulation of the Evolution of Gene Families	p. 492
Computer Analysis of Evolution of Gene Families Coding for Proteins	p. 496
Classification of Evolution Modes of Gene Families Coding for Proteins	p. 496
Analysis of Change in Amino Acid Physical and Chemical Properties during the Evolution of Gene Families	p. 500
Theoretical Investigation of Regulatory Contours Evolution under Various Types of Selection	p. 503
Some Evolutionary Properties of the Simplest Regulatory Mechanism of Negative Feedback Type	p. 504
Protein Evolution in Systems with Feedbacks under Various Types of Selection	p. 506
Regulatory Mechanisms and the Problem of the Neutrality-Adaptivity of Molecular Evolution	p. 510
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