000			07232cam a2200289 a 4500
001			14042651
005			20220626153919.0
008			050719s2005 enka b 001 0 eng
010			_a 2005279076
020			_a9780199277872
040			_aDLC _cDLC _dDLC _dEG-CaNU
082			_2570.285 _a21
100	1		_aLesk, Arthur M. _cauthor.
245	1	0	_aIntroduction to bioinformatics / _cArthur M. Lesk.
246	3	0	_aBioinformatics
250			_a2nd ed.
260			_aOxford ; _aNew York : _bOxford University Press, _c2005.
300			_axviii, 360 p., 10 p. of plates : _bill. (some col.) ; _c25 cm.
504			_aIncludes bibliographical references and index.
505			_a1 Introduction 1 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 24 Use of SINES and LINES to derive phylogenetic relationships 30 Searching for similar sequences in databases: PSI-BLAST 32 Introduction to protein structure 40 The hierarchical nature of protein architecture 41 Classification of protein structures 44 Protein structure prediction and engineering 51 Critical Assessment of Structure Prediction (CASP) 52 Protein engineering 52 Proteomics 52, DNA microarrays 53 Mass spectrometry 54 Systems biology 54 Clinical implications 55 The future 57 Recommended reading 57 Exercises, Problems, and Weblems 59 2 Genome organization and evolution 67 Genomes and proteomes 68 Genes 69 Proteomes 71 Eavesdropping on the transmission of genetic information 72 Mappings between the maps 77 High-resolution maps 78 Picking out genes in genomes 80 Genomes of prokaryotes 81 The genome of the bacterium Escherichia coil 82 The genome of the archaeon Methanococcusjannaschii 85 The genome of one of the simplest organisms: Mycoplasma genitalium 86 Genomes of eukaryotes 87 The genome of Saccharomyces cerevisiae (baker's yeast) 89 The genome of Caenorhabditis elegans 93 The genome of Drosophila melanogaster 94 The genome of Arabidopsis thaliana 95 The genome of Homo sapiens (the human genome) 96 Protein coding genes 97 Repeat sequences 99 RNA 100 Single-nucleotide polymorphisms (SNPs) 101 Genetic diversity in anthropology 102 Genetic diversity and personal identification 103 Genetic analysis of cattle domestication .104 Evolution of genomes 104 Please pass the genes: horizontal gene transfer 108 Comparative genomics of eukaryotes 109 Recommended reading 111 Exercises, Problems, and Weblems 112 3 Archives and information retrieval 117 Introduction 118 Database indexing and specification of search terms 118 Follow-up questions 120 Analysis of retrieved data 121 The archives 121 Nucleic acid sequence databases 122 Genome databases 124 Protein sequence databases 124 Databases of structures 128 Specialized, or'boutique' databases 135 Expression and proteomics databases 136 Databases of metabolic pathways 138 Bibliographic databases 139 Surveys of molecular biology databases and servers 139 Gateways to archives 140 Access to databases in molecular biology 141 ENTREZ 141 The Sequence Retrieval System (SRS) 148 The Protein Identification Resource (PIR) 149 ExPASy-Expert Protein Analysis System 150 Ensembl 151 Where do we go from here? 152 Recommended reading 152 Exercises, Problems, and Weblems 153 4 Alignments and phylogenetic trees 157 Introduction to sequence alignment 158 The dotplot 160 Dotplots and sequence alignments 165 Measures of sequence similarity 171 Scoring schemes 171 Computing the alignment of two sequences 175 Variations and generalizations 175 Approximate methods for quick screening of databases 176 The dynamic programming algorithm for optimal pairwise sequence alignment 176 Significance of alignments 182 Multiple sequence alignment 186 Applications of multiple sequence alignments to database searching 188 Profiles 189 PSI-BLAST 191 Hidden Markov Models 193 Phylogeny 198 Phylogenetic trees 203 Clustering methods 205 Cladistic methods 206 The problem of varying rates of evolution 207 Computational considerations 208 Recommended reading 209 Exercises, Problems, and Weblems 210 5 Protein structure and drug discovery 219 Introduction 220 Protein stability and folding 223 The Sasisekharan-Ramakrishnan-Ramachandran plot describes allowed mainchain conformations 223 The sidechains 225 Protein stability and denaturation 225 Protein folding 228 Applications of hydrophobicity 229 Superposition of structures, and structural alignments 233 DALI (Distance-matrix ALignment) 235 Evolution of protein structures 236 Classifications of protein structures 238 SCOP 239 Protein structure prediction and modelling 240 Critical Assessment of Structure Prediction (CASP) 242 Secondary structure prediction 244 Homology modelling 250 Fold recognition 252 Conformational energy calculations and molecular dynamics 255 ROSETTA 259 LINUS 259 Assignment of protein structures to genomes 263 Prediction of protein function 265 Divergence of function: orthologues and paralogues 266 Drug discovery and development 269 The lead compound 271 Bioinformatics in drug discovery and development 273 Recommended reading 284 Exercises, Problems, and Weblems 285 6 Proteomics and systems biology 291 DNA microarrays 293 Analysis of microarray data 295 Mass spectrometry 301 Identification of components of a complex mixture 301 Protein sequencing by mass spectrometry 304 Genome sequence analysis by mass spectrometry 306 Systems biology 311 Networks and graphs 313 Network structure and dynamics 318 Protein complexes and aggregates 320 Properties of protein-protein complexes 321 Protein interaction networks 324 Regulatory networks 329 Structures of regulatory networks 330 Structural biology of regulatory networks 336 Recommended reading 339 Exercises, Problems, and Weblems 339 Conclusions 345 Answers to Exercises 347 Glossary 353 Index 357 Colour plates
520			_a the second edition of Introduction to Bioinformatics introduces the student to the power of bioinformatics as a set of scientific tools. Retaining and enhancing the rich pedagogy and lucid presentation of the first edition, this new edition explains how to access the data archives of genomes and proteins, and the kind of questions these data and tools can answer. It also discusses how to make inferences from the data archives, how to make connections among them, and how to derive useful and interesting predictions. The book is accompanied by a fully integrated companion website.
650		0	_aBioinformatics.
942			_2ddc _cBK
999			_c9702 _d9702