Holdings: Introduction to bioinformatics

Introduction to bioinformatics:

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Bibliographic Details
Main Author:	Lesk, Arthur M. (Author)
Format:	Book
Language:	English
Published:	Oxford [u.a.] Oxford Univ. Press 2008
Edition:	3. ed.
Subjects:	Bioinformatics Computational Biology Bioinformatik Lehrbuch
Online Access:	Inhaltsverzeichnis
Physical Description:	XXII, 474 S., [4] Bl. Ill., graph. Darst.
ISBN:	9780199208043

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adam_text	Contents 1 Introduction ι Life in space and time 3 Evolution is the change over time in the world of living things 4 Dogmas: central and peripheral 6 Observables and data archives 9 Information flow in bioinformatics 12 Curation, annotation and quality control 13 The World Wide Web 14 Electronic publication 15 Computers and computer science 16 Programming 17 Biological classification and nomenclature 21 Use of sequences to determine phylogenetic relationships 22 Use of SINES and LINES to derive phylogenetic relationships 31 Searching for similar sequences in databases: PSI-BLAST 33 Introduction to protein structure 42 The hierarchical nature of protein architecture 43 Classification of protein structures 46 Protein structure prediction and engineering 52 Critical Assessment of Structure Prediction (CASP) 53 Protein engineering 53 Proteomics 54 DNA microarrays 54 Systems biology 56 Clinical implications 56 The future 59 Recommended reading 59 Exercises, Problems and Weblems 61 2 Genome organization and evolution ω Genomes and proteomes 70 Genes 70 Proteomics 73 Eavesdropping on the transmission of genetic information 74 Identification of genes associated with inherited diseases 76 Mappings between the maps 77 xviii CONTENTS High-resolution maps 80 Picking out genes in genomes Ш Genome sequencing projects 83 Genomes on the Web 84 Genomes of prokaryotes 86 The genome of the bacterium Escherichia coli 87 The genome of the archaeon Methanococcus jannaschii 90 The genome of one of the simplest organisms: Mycoplasma genitalium 91 Genomes of eukarya 92 Gene families 95 The genome of Saccharomyces cerevisiae (Baker s yeast) 97 The genome of Caenorhabdkis elegans 98 The genome of Drosophila melanogaster 101 The genome of Arab/dops/s thaííana 101 The genome of Homo sapiens (The Human Genome) 104 Protein-coding genes 104 Repeat sequences 107 RNA 108 Single-nudeotide polymorphisms (SNPs) and haplotypes 108 Systematic measurements and collections of SNPs 111 Genetic diversity in anthropology 113 Genetic diversity and personal identification 116 Evolution of genomes 116 Please pass the genes: horizontal gene transfer 121 Comparative genomics of eukarya 123 The ENCODE project 124 Metagenomics: the collection of genomes in a coherent environmental sample 128 Recommended reading 131 Exercises, Problems and Weblems 132 3 Scientific publications and archives: media, content and access m The scientific literature 138 Economic factors governing access to scholarly publications 139 Open access 141 The Public Library of Science (PLoS) 142 Traditional and digital libraries 143 How to populate a digital library 244 The information explosion 145 The Web—higher dimensions 145 New media — video, sound 146 Searching the literature 146 Bibliography management 247 CONTENTS ХІХ Databases 148 Database contents 148 The literature as a database 149 Organization 149 Annotation 152 Database quality control 153 Database access 356 Links 157 Database interoperability 359 Data mining 362 Programming languages and tools 365 Traditional programming languages 366 Scripting languages 366 Program libraries specialized for molecular biology 167 Java — computing over the Web 367 Markup languages 368 Natural language processing 170 Identifying keywords and combinations of keywords 373 Knowledge extraction: protein-protein interactions 172 Applications of text mining 174 Recommended reading 181 Exercises, Problems and Weblems 182 4 Archives and information retrieval ish Database indexing and specification of search terms 387 The archives 390 Nucleic acid sequence databases 390 Genome databases and genome browsers 392 Protein sequence databases 393 Databases of protein families 298 Databases of structures 399 Classifications of protein structures 204 Accuracy and precision of protein structure determinations 204 Classification and assignment of protein function 206 The Enzyme Commission 206 The Gene Ontology Consortium protein function classification 207 Specialized, or boutique databases 230 Expression and proteomics databases 233 Databases of metabolic pathways 233 Bibliographic databases 238 Surveys of molecular biology databases and servers 238 Gateways to archives 219 Access to databases in molecular biology 220 ENTREZ 220 The Sequence Retrieval System (SRS) 233 XX CONTENTS The Protein Identification Resource (PIR) 234 ExPASy— Expert Protein Analysis System 236 Where do we go from here? 237 Recommended reading 237 Exercises, Problems and Weblems 237 5 Alignments and phylogenetic trees 242 Introduction to sequence alignment 243 Thedotplot 244 Dotplots and sequence alignments 249 Measures of sequence similarity 254 Scoring schemes 255 Derivation of substitution matrices: РАМ matrices 256 Computing the alignment of two sequences 258 Variations and generalizations 259 Approximate methods for quick screening of databases 259 The dynamic-programming algorithm for optimal pairwise sequence alignment 261 Significance of alignments 267 Multiple sequence alignment 271 Applications of multiple sequence alignments to database searching 273 Profiles 273 PSI-BLAST 276 Hidden Markov Models 278 Phylogeny 281 Determination of taxonomie relationships from molecular properties 284 Phylogenetic trees 286 Clustering methods 288 Cladistic methods 290 Reconstruction of ancestral sequences 291 The problem of varying rates of evolution 293 Are trees the correct way to present phylogenetic relationships? 294 Computational considerations 296 Putting it all together 296 Recommended reading 297 Exercises, Problems and Weblems 298 6 Structural bioinformatics and drug discovery 307 Introduction 308 Protein stability and folding 310 The Sasisekharan-Ramakrishnan-Ramachandran plot describes allowed mainchain conformations 310 The sidechains 312 Protein stability and denaturation 314 Protein folding 326 CONTENTS XXI Applications of hydrophobicity 317 Coiled-coil proteins 321 Superposition of structures, and structural alignments 324 DALI and MUSTANG 326 Evolution of protein structures 327 Classifications of protein structures 330 Protein structure prediction and modelling 333 A priori and empirical methods 334 Critical Assessment of Structure Prediction (CASP) 337 Secondary structure prediction 338 Homology modelling 343 Fold recognition 345 Conformational energy calculations and molecular dynamics 351 Assignment of protein structures to genomes 358 Prediction of protein function 360 Divergence of function: orthologues and paralogues 362 Drug discovery and development 364 The lead compound 367 Improving on the lead compound: quantitative structure-activity relationships (QSAR) 367 Bioinformatics in drug discovery and development 369 Molecular modelling in drug discovery 370 Recommended reading 379 Exercises, Problems and Web/ems 380 Proteomics and systems biology звэ DNA microarrays 390 Analysis of microarray data 392 Mass spectrometry 398 Identification of components of a complex mixture 399 Protein sequencing by mass spectrometry 402 Measuring deuterium exchange in proteins 404 Genome sequence analysis by mass spectrometry 404 Systems biology 409 Protein complexes and aggregates 411 Properties of protein-protein complexes 432 Protein interaction networks 415 Networks and graphs 420 Dynamics, stability and robustness 424 The background of systems biology: sources of ideas 426 Complexity of sequences 427 Computational complexity 430 Static and dynamic complexity 432 Chaos and predictability 433 xxii CONTENTS Alignment of metabolic pathways 434 Regulatory networks 438 Signal transduction and transcriptional control 441 Structures of regulatory networks 441 Structural biology of regulatory networks 441 The genetic switch of bacteriophage λ 443 The genetic regulatory network of Saccharomyces cerevisiae 451 Adaptability of the yeast regulatory network 454 Recommended reading 456 Exercises, Problems and Weblems 456 Conclusions 465 Index 467 Colour Plates 475
adam_txt	Contents 1 Introduction ι Life in space and time 3 Evolution is the change over time in the world of living things 4 Dogmas: central and peripheral 6 Observables and data archives 9 Information flow in bioinformatics 12 Curation, annotation and quality control 13 The World Wide Web 14 Electronic publication 15 Computers and computer science 16 Programming 17 Biological classification and nomenclature 21 Use of sequences to determine phylogenetic relationships 22 Use of SINES and LINES to derive phylogenetic relationships 31 Searching for similar sequences in databases: PSI-BLAST 33 Introduction to protein structure 42 The hierarchical nature of protein architecture 43 Classification of protein structures 46 Protein structure prediction and engineering 52 Critical Assessment of Structure Prediction (CASP) 53 Protein engineering 53 Proteomics 54 DNA microarrays 54 Systems biology 56 Clinical implications 56 The future 59 Recommended reading 59 Exercises, Problems and Weblems 61 2 Genome organization and evolution ω Genomes and proteomes 70 Genes 70 Proteomics 73 Eavesdropping on the transmission of genetic information 74 Identification of genes associated with inherited diseases 76 Mappings between the maps 77 xviii CONTENTS High-resolution maps 80 Picking out genes in genomes Ш Genome sequencing projects 83 Genomes on the Web 84 Genomes of prokaryotes 86 The genome of the bacterium Escherichia coli 87 The genome of the archaeon Methanococcus jannaschii 90 The genome of one of the simplest organisms: Mycoplasma genitalium 91 Genomes of eukarya 92 Gene families 95 The genome of Saccharomyces cerevisiae (Baker's yeast) 97 The genome of Caenorhabdkis elegans 98 The genome of Drosophila melanogaster 101 The genome of Arab/dops/s thaííana 101 The genome of Homo sapiens (The Human Genome) 104 Protein-coding genes 104 Repeat sequences 107 RNA 108 Single-nudeotide polymorphisms (SNPs) and haplotypes 108 Systematic measurements and collections of SNPs 111 Genetic diversity in anthropology 113 Genetic diversity and personal identification 116 Evolution of genomes 116 Please pass the genes: horizontal gene transfer 121 Comparative genomics of eukarya 123 The ENCODE project 124 Metagenomics: the collection of genomes in a coherent environmental sample 128 Recommended reading 131 Exercises, Problems and Weblems 132 3 Scientific publications and archives: media, content and access m The scientific literature 138 Economic factors governing access to scholarly publications 139 Open access 141 The Public Library of Science (PLoS) 142 Traditional and digital libraries 143 How to populate a digital library 244 The information explosion 145 The Web—higher dimensions 145 New media — video, sound 146 Searching the literature 146 Bibliography management 247 CONTENTS ХІХ Databases 148 Database contents 148 The literature as a database 149 Organization 149 Annotation 152 Database quality control 153 Database access 356 Links 157 Database interoperability 359 Data mining 362 Programming languages and tools 365 Traditional programming languages 366 Scripting languages 366 Program libraries specialized for molecular biology 167 Java — computing over the Web 367 Markup languages 368 Natural language processing 170 Identifying keywords and combinations of keywords 373 Knowledge extraction: protein-protein interactions 172 Applications of text mining 174 Recommended reading 181 Exercises, Problems and Weblems 182 4 Archives and information retrieval ish Database indexing and specification of search terms 387 The archives 390 Nucleic acid sequence databases 390 Genome databases and genome browsers 392 Protein sequence databases 393 Databases of protein families 298 Databases of structures 399 Classifications of protein structures 204 Accuracy and precision of protein structure determinations 204 Classification and assignment of protein function 206 The Enzyme Commission 206 The Gene Ontology Consortium protein function classification 207 Specialized, or 'boutique' databases 230 Expression and proteomics databases 233 Databases of metabolic pathways 233 Bibliographic databases 238 Surveys of molecular biology databases and servers 238 Gateways to archives 219 Access to databases in molecular biology 220 ENTREZ 220 The Sequence Retrieval System (SRS) 233 XX CONTENTS The Protein Identification Resource (PIR) 234 ExPASy— Expert Protein Analysis System 236 Where do we go from here? 237 Recommended reading 237 Exercises, Problems and Weblems 237 5 Alignments and phylogenetic trees 242 Introduction to sequence alignment 243 Thedotplot 244 Dotplots and sequence alignments 249 Measures of sequence similarity 254 Scoring schemes 255 Derivation of substitution matrices: РАМ matrices 256 Computing the alignment of two sequences 258 Variations and generalizations 259 Approximate methods for quick screening of databases 259 The dynamic-programming algorithm for optimal pairwise sequence alignment 261 Significance of alignments 267 Multiple sequence alignment 271 Applications of multiple sequence alignments to database searching 273 Profiles 273 PSI-BLAST 276 Hidden Markov Models 278 Phylogeny 281 Determination of taxonomie relationships from molecular properties 284 Phylogenetic trees 286 Clustering methods 288 Cladistic methods 290 Reconstruction of ancestral sequences 291 The problem of varying rates of evolution 293 Are trees the correct way to present phylogenetic relationships? 294 Computational considerations 296 Putting it all together 296 Recommended reading 297 Exercises, Problems and Weblems 298 6 Structural bioinformatics and drug discovery 307 Introduction 308 Protein stability and folding 310 The Sasisekharan-Ramakrishnan-Ramachandran plot describes allowed mainchain conformations 310 The sidechains 312 Protein stability and denaturation 314 Protein folding 326 CONTENTS XXI Applications of hydrophobicity 317 Coiled-coil proteins 321 Superposition of structures, and structural alignments 324 DALI and MUSTANG 326 Evolution of protein structures 327 Classifications of protein structures 330 Protein structure prediction and modelling 333 A priori and empirical methods 334 Critical Assessment of Structure Prediction (CASP) 337 Secondary structure prediction 338 Homology modelling 343 Fold recognition 345 Conformational energy calculations and molecular dynamics 351 Assignment of protein structures to genomes 358 Prediction of protein function 360 Divergence of function: orthologues and paralogues 362 Drug discovery and development 364 The lead compound 367 Improving on the lead compound: quantitative structure-activity relationships (QSAR) 367 Bioinformatics in drug discovery and development 369 Molecular modelling in drug discovery 370 Recommended reading 379 Exercises, Problems and Web/ems 380 Proteomics and systems biology звэ DNA microarrays 390 Analysis of microarray data 392 Mass spectrometry 398 Identification of components of a complex mixture 399 Protein sequencing by mass spectrometry 402 Measuring deuterium exchange in proteins 404 Genome sequence analysis by mass spectrometry 404 Systems biology 409 Protein complexes and aggregates 411 Properties of protein-protein complexes 432 Protein interaction networks 415 Networks and graphs 420 Dynamics, stability and robustness 424 The background of systems biology: sources of ideas 426 Complexity of sequences 427 Computational complexity 430 Static and dynamic complexity 432 Chaos and predictability 433 xxii CONTENTS Alignment of metabolic pathways 434 Regulatory networks 438 Signal transduction and transcriptional control 441 Structures of regulatory networks 441 Structural biology of regulatory networks 441 The genetic switch of bacteriophage λ 443 The genetic regulatory network of Saccharomyces cerevisiae 451 Adaptability of the yeast regulatory network 454 Recommended reading 456 Exercises, Problems and Weblems 456 Conclusions 465 Index 467 Colour Plates 475
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title	Introduction to bioinformatics
title_alt	Bioinformatics
title_auth	Introduction to bioinformatics
title_exact_search	Introduction to bioinformatics
title_exact_search_txtP	Introduction to bioinformatics
title_full	Introduction to bioinformatics Arthur M. Lesk
title_fullStr	Introduction to bioinformatics Arthur M. Lesk
title_full_unstemmed	Introduction to bioinformatics Arthur M. Lesk
title_short	Introduction to bioinformatics
title_sort	introduction to bioinformatics
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topic_facet	Bioinformatics Computational Biology Bioinformatik Lehrbuch
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