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Introduction To Bioinformatics

by: Lesk, Arthur M.

Introduction To Bioinformatics

by: Lesk, Arthur M.

ISBN 13:
9780199277872
ISBN 10:
0199277877
Edition: 2nd
Format: Paperback
Copyright: 05/12/2005
Publisher: Oxford University Press
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Summary

On 26 June 2000, the completion of the draft sequence of the Human Genome saw the sciences of biology and medicine change forever. It promised new insights into how our genes shape who we are, and how we function. At the heart of this breakthrough lies a scientific discipline that is now one of the most important knowledge-building tools in current molecular and cellular biology, and healthcare development: bioinformatics.

Plan of the book

xix

Introduction

(66)

Life in space and time

(1)

Evolution is the change over time in the world of living things

(2)

Dogmas: central and peripheral

(3)

Observables and data archives

(5)

Information flow in bioinformatics

(1)

Curation, annotation, and quality control

(1)

The World Wide Web

(2)

Electronic publication

(1)

Computers and computer science

(5)

Programming

(4)

Biological classification and nomenclature

(3)

Use of sequences to determine phylogenetic relationships

(8)

Use of SINES and LINES to derive phylogenetic relationships

(2)

Searching for similar sequences in databases: PSI-BLAST

(8)

Introduction to protein structure

(11)

The hierarchical nature of protein architecture

(3)

Classification of protein structures

(7)

Protein structure prediction and engineering

(1)

Critical Assessment of Structure Prediction (CASP)

(1)

Protein engineering

(1)

Proteomics

(3)

DNA microarrays

(1)

Mass spectrometry

(1)

Systems biology

(1)

Clinical implications

(12)

The future

(1)

Recommended reading

(2)

Exercises, Problems, and Weblems

(8)

Genome organization and evolution

(50)

Genomes and proteomes

(4)

Genes

(2)

Proteomes

(1)

Eavesdropping on the transmission of genetic information

(8)

Mappings between the maps

(1)

High-resolution maps

(2)

Picking out genes in genomes

(1)

Genomes of prokaryotes

(6)

The genome of the bacterium Escherichia coli

(3)

The genome of the archaeon Methanococcus jannaschii

(1)

The genome of one of the simplest organisms: Mycoplasma genitalium

(1)

Genomes of eukaryotes

(9)

The genome of Saccharomyces cerevisiae (baker's yeast)

(4)

The genome of Caenorhabditis elegans

(1)

The genome of Drosophila melanogaster

(1)

The genome of Arabidopsis thaliana

(1)

The genome of Homo sapiens (the human genome)

(5)

Protein coding genes

(2)

Repeat sequences

(1)

RNA

100

(1)

Single-nucleotide polymorphisms (SNPs)

101

(1)

Genetic diversity in anthropology

102

(2)

Genetic diversity and personal identification

103

(1)

Genetic analysis of cattle domestication

104

(1)

Evolution of genomes

104

(13)

Please pass the genes: horizontal gene transfer

108

(1)

Comparative genomics of eukaryotes

109

(2)

Recommended reading

111

(1)

Exercises, Problems, and Weblems

112

(5)

Archives and information retrieval

117

(40)

Introduction

118

(3)

Database indexing and specification of search terms

118

(2)

Follow-up questions

120

(1)

Analysis of retrieved data

121

(1)

The archives

121

(19)

Nucleic acid sequence databases

122

(2)

Genome databases

124

(1)

Protein sequence databases

124

(4)

Databases of structures

128

(7)

Specialized, or `boutique' databases

135

(1)

Expression and proteomics databases

136

(2)

Databases of metabolic pathways

138

(1)

Bibliographic databases

139

(1)

Surveys of molecular biology databases and servers

139

(1)

Gateways to archives

140

(12)

Access to databases in molecular biology

141

(1)

Entrez

141

(7)

The Sequence Retrieval System (SRS)

148

(1)

The Protein Identification Resources (PIR)

149

(1)

ExPASy---Expert Protein Analysis System

150

(1)

Ensembl

151

(1)

Where do we go from here?

152

(5)

Recommended reading

152

(1)

Exercises, Problems, and Weblems

153

(4)

Alignments and phylogenetic trees

157

(62)

Introduction to sequence alignment

158

(2)

The dotplot

160

(5)

Dotplots and sequence alignments

165

(6)

Measures of sequence similarity

171

(4)

Scoring schemes

171

(4)

Computing the alignment of two sequences

175

(1)

Variations and generalizations

175

(1)

Approximate methods for quick screening of databases

176

(1)

The dynamic programming algorithm for optimal pairwise sequence alignment

176

(6)

Significance of alignments

182

(4)

Multiple sequence alignment

186

(2)

Applications of multiple sequence alignments to database searching

188

(10)

Profiles

189

(2)

PSI-BLAST

191

(2)

Hidden Markov Models

193

(5)

Phylogeny

198

(5)

Phylogenetic trees

203

(16)

Clustering methods

205

(1)

Cladistic methods

206

(1)

The problem of varying rates of evolution

207

(1)

Computational considerations

208

(1)

Recommended reading

209

(1)

Exercises, Problems, and Weblems

210

(9)

Protein structure and drug discovery

219

(72)

Introduction

220

(3)

Protein stability and folding

223

(6)

The Sasisekharan-Ramakrishnan-Ramachandran plot describes allowed mainchain conformations

223

(2)

The sidechains

225

(1)

Protein stability and denaturation

225

(3)

Protein folding

228

(1)

Applications of hydrophobicity

229

(4)

Superposition of structures, and structural alignments

233

(2)

DALI (Distance-matrix ALIgnment)

235

(1)

Evolution of protein structures

236

(2)

Classifications of protein structures

238

(2)

SCOP

239

(1)

Protein structure prediction and modelling

240

(23)

Critical Assessment of Structure Prediction (CASP)

242

(2)

Secondary structure prediction

244

(6)

Homology modelling

250

(2)

Fold recognition

252

(3)

Conformational energy calculations and molecular dynamics

255

(4)

Rosetta

259

(1)

Linus

259

(4)

Assignment of protein structures to genomes

263

(2)

Prediction of protein function

265

(4)

Divergence of function: orthologues and paralogues

266

(3)

Drug discovery and development

269

(22)

The lead compound

271

(2)

Bioinformatics in drug discovery and development

273

(11)

Recommended reading

284

(1)

Exercises, Problems, and Weblems

285

(6)

Proteomics and systems biology

291

(54)

DNA microarrays

293

(8)

Analysis of microarray data

295

(6)

Mass spectrometry

301

(10)

Identification of components of a complex mixture

301

(3)

Protein sequencing by mass spectrometry

304

(2)

Genome sequence analysis by mass spectrometry

306

(5)

Systems biology

311

(2)

Networks and graphs

313

(7)

Network structure and dynamics

318

(2)

Protein complexes and aggregates

320

(4)

Properties of protein-protein complexes

321

(3)

Protein interaction networks

324

(5)

Regulatory networks

329

(16)

Structures of regulatory networks

330

(6)

Structural biology of regulatory networks

336

(3)

Recommended reading

339

(1)

Exercises, Problems, and Weblems

339

(6)

Conclusions

345

(2)

Answers to Exercises

347

(6)

Glossary

353

(4)

Index

357

Amazon no longer offers textbook rentals. We do!

Introduction To Bioinformatics

Introduction To Bioinformatics

9780199277872

0199277877

Summary

Table of Contents

Supplemental Materials

Write a Review

Amazon no longer offers textbook rentals. We do!

Introduction To Bioinformatics

Introduction To Bioinformatics

9780199277872

0199277877

Summary

Table of Contents

Supplemental Materials

Write a Review

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