Introduction to bioinformatics:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Oxford [u.a.]
Oxford Univ. Press
2014
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| Edition: | 4. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVI, 371 S. Ill., graph. Darst. |
| ISBN: | 9780199651566 0199651566 |
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Record in the Search Index
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| adam_text | Titel: Introduction to bioinformatics
Autor: Lesk, Arthur M
Jahr: 2014
CONTENTS
Preface to the first edition xiv
Preface to the second edition xvü
Preface to the third edition xviü
Preface to the fourth edition xix
Plan of the book xx
Introduction to bioinformatics on the web xxi
Acknowledgements xxü
Introduction 1
Life in space and time 3
Phenotype = genotype + environment + life history + epigenetics 4
Evolution is the change over time in the world of living things 4
Dogmas; central and peripheral ¦ 6
Statics and dynamics 9
Networks 10
Observables and data archives .10
A database without effective modes of access is merely a data graveyard 12
Information flow in bioinformatics 12
Curation, annotation, and quality control 14
The worfd-wide web 15
Electronic publication 16
Computers and Computer science 16
Programming 17
Biological Classification and nomenclature 21
Use of sequences to determine phyiogenetic relationships 23
Use of SINES and LINES to derive phylogenetic relationships 29
Searching for similar sequences in databases; PSl-BLAST 30
Introduction to protein structure 38
The hierarchicai nature of prbtein architecture 40
Classification of protein structures 41
Protein structure prediction and engineering 46
Critical Assessment of Structure Prediction 47
Protein engineering 48
Proteomics and transcriptomics 48
DNA microarrays 49
Transcriptomics and RNA sequencing 50
Mass spectrometry 50
^^m
Contents
Systems biology 50
Clinical implications 50
The future 53
Recommended reading 53
Exercises and problems 55
2 Genome Organization and evolution 59
Genomes, transcriptomes, and proteomes 59
Genes 60
Proteomics and transcriptomics 62
Eavesdropping on the Transmission of genetic Information 64
Identification of genes associated with inherited diseases 64
Mappings between the maps 66
High-resolution maps 68
Genome-wide association studies 69
Picking out genes in genomes 70
Genome-sequencing projects 71
Genomes of prokaryotes 72
The genome of the bacterium Escherichia coli 73
The genome of the archaeon Methanococcus /annasch// 75
The genome of one of the simplest organisms: Mycoplasma genitalium 76
AAetagenomics: the collection of genomes in a coherent environmental sample 76
The human microbiome 79
Genomes of eukarya 79
Gene families 82
The genome of Saccharomyces cerevisiae (baker s yeast) 82
The genome of Caenorhabditis elegans 84
The genome of Drosophila melanogaster 85
The genome of Arabidopsis thaliana 86
The genome of Homo sapiens (the human genome) 88
Protein-coding genes 88
Repeat sequences 89
RNA 90
Single-nucleotide polymorphisms and haplotypes 90
Systematic measurements and collections of single-nucleotide polymorphisms 92
Ethical, legal, and social issues 94
Genetic diversity in anthropology 95
DNA sequences and languages 96
Genetic diversity and personal Identification 97
Evolution of genomes 98
Please pass the genes: horizontal gene transfer 10°
Comparative genomics of eukarya 10 1
Recommended Reading 1°2
Contents
Exercises and problems 103
3 Scientific publications and archives: media, content, and access 107
The scientific literature 107
Economic factors governing access to scholarly publications 109
Open access 110
The Public Library of Science 111
Traditional and digital libraries 111
How to populate a digital library 112
The Information explosion 113
The web: higher dimensions 113
New media: Video, sound 113
Searching the literature 114
Bibliography management 114
Databases 115
Database contents 116
The literature as a database 116
Database Organization 116
Annotation 119
Database quality control 120
Database access 122
Links 123
Database interoperability 125
Datamining 127
Programming languages and tools 128
Traditional programming languages 130
Scripting languages 130
Program libraries specialized for molecular biology 130
Java: Computing over the web 131
Markup languages 131
Natural language processing 133
Natural language processing and mining the biomedical literature 134
Applications of text mining 136
Recommended reading 141
Exercises and problems 142
4 Archives and Information retrieval 144
Database indexing and specification of search terms 144
Follow-up questions 145
Analysis and processing of retrieved data 146
The archives 146
Nucleic acid sequence databases 147
Genome databases and genome browsers 148
Protein sequence databases 149
Databases of protein families 152
Contents
Databases of structures 153
Classifications of protein structures 157
Accuracy and precision of protein structure determinations 157
Specialized, or boutique , databases 158
Expression and proteomics databases 159
Bibliographie databases 160
Surveys of molecular biology databases and Servers 161
Gateways to archives • 161
Access to databases in molecular biology 162
ENTREZ 162
The Protein Identification Resource 171
ExPASy: Expert Protein Analysis System 172
Where do we go from here? 173
Recommended reading 173
Exercises and problems , 174
Alignments and phylogenetic trees 175
introduction to sequence alignment 175
Thedotplot 176
Dotplots and sequence alignments 181
Measures of sequence similarity 182
Scoring schemes 184
Derivation of Substitution matrices: PAM and BLOSUM matrices 184
Computing the alignment of two sequences 187
Variations and generalizations 187
Approximate methods for quick Screening of databases 188
The dynamic-programming algorithm for optimal pairwise
sequence alignment 188
Significance of alignments 194
Multiple sequence alignment 196
Applications of multiple sequence alignments and database searching 198
Profiles 198
PSI-BLAST 200
Hidden Markov modeis 201
Phylogersy 203
Determination of taxonomic relationships from molecular properties 205
Phylogenetic trees 207
Clustering methods 209
Ciadistic methods 210
Reconstruction of ancestral sequences 211
The problem of varying rates of evolution 213
Are trees the correct way to present phylogenetic relationships? 213
Computational considerations 214
Putting it all together 215
Contents
Recommended reading 215
Exercises and problems 216
Structural bioinformatics and drug discovery 222
Introduction 222
Protein stability and folding 224
The Sasisekharan-Ramakrishnan-Ramachandran plot describes
allowed mainchain conformations 225
The sidechains 226
Protein stability and denaturation 227
Protein folding 229
Applications of hydrophobicity 230
Coiled-coiled proteins 230
Superposition of structures, and structural alignments 235
DALI and MUSTANG 237
Evolution of protein structures 238
Classifications of protein structures 240
Protein structure prediction and modelling 241
A priori and empirical methods 241
Critical Assessment of Structure Prediction 243
Secondary structure prediction 246
Homology modelling 249
Fold recognition v 250
Conformational energy calculations and molecular dynamics 255
Assignment of protein structures to genomes 260
Prediction of protein function 261
Divergence of function: orthologues and paralogues 261
Drug discovery and development 264
The lead Compound 265
Improving on the lead Compound: quantitative structure-activity relationships 266
Bioinformatics in drug discovery and development 267
Molecular modelling in drug discovery 268
Recommended reading 274
Exercises and problems 276
Introduction to Systems biology 282
Introduction 282
Networks and graphs 284
Connectivity in networks 285
Dynamics, stability, and robustness 286
Some sources of ideas for Systems biology 288
Complexity of sequences 288
Computational complexity 291
Contents
Static and dynamic complexity 291
Chaos and predictability 293
Recommended reading 294
Exercises and problems 294
8 Metabolie pathways 297
Classification and assignment of protein function 298
The Enzyme Commission 298
The Gene Ontology Consortium protein function Classification 299
Catalysis by enzymes 301
Active Sites 303
Cofactors 303
Protein-ligand binding equilibria 304
Enzyme kinetics 305
Measures of effectiveness of enzymes 306
How do proteins evolve new functions? 307
Control over enzyme activity 308
Structural mechanisms of evolution of altered or novel protein functions 308
Protein evolution at the level of domain assembly 311
Databases of metabolic pathways 312
EcoCyc 313
The Kyoto Encyclopedia of Genes and Genomes 313
Evolution and phylogeny of metabolic pathways 316
Pathway com parison 316
Alignment of metabolic pathways 320
Comparing linear metabolic pathways 320
Comparing nonlinear metabolic pathways: the pentose phosphate
pathway and the Calvin-Benson cycle 321
Dynamics of metabolic networks 322
Robustness of metabolic networks 323
Dynamic modelling of metabolism 324
Recommended reading 326
Exercises and problems 326
9 Gene expression and regulation 328
DNA microarrays 329
Microarray data are quantitative but imprecise 330
Analysis of microarray data 330
Mass spectrometry 335
Identification of components of a complex mixture 335
Protein sequencing by mass spectrometry 337
Measuring deuterium exchange in proteins 338
Genome sequence analysis by mass spectrometry 339
Contents
Protein complexes and aggregates 342
Properties of protein-protein complexes 343
Protein interaction networks 345
Regulatory networks 348
Signal transduction and transcriptional control 349
Structures of regulatory networks 350
Structural biology of regulatory networks 350
The genetic switch of bacteriophage X 352
What are the characteristics of the switch that must be implemented
by DNA-protein interacBons? 353
The materials 354
How to throw the switch 355
The genetic regulatory network of Saccharomyces cerevisiae 356
Adaptability of the yeast regulatory network 358
Recommended reading 360
Exercises and problems 360
Conclusion 363
Index 365
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| title_full_unstemmed | Introduction to bioinformatics Arthur M. Lesk |
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