Enhanced descriptions from Syndetics:

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 our genetic make-up, how our genes shape who we are, and how we function, and new possibilities for an improved quality of life, exploiting new knowledge to design novel, more effective drugs. At the heart of this breakthrough lies a scientific discipline which is now one of the most important information gathering, data-mining, and knowledge-building tools in current research and healthcare development: bioinformatics.Written by a pioneer of the use of bioinformatics in research, Introduction to Bioinformatics 2/e introduces the student to the power of bioinformatics as a set of scientific tools. The book explains how to access the data archives of genomes and proteins, and the kind of questions these data and tools can answer - how to make inferences from the data archives, to make connections among them, and to derive useful and interesting predictions.Retaining and enhancing the rich pedagogy and lucid presentation of the first edition, the book is accompanied by a fully integrated Online Resource Centre, encouraging students to explore the computational tools of bioinformatics in a relevant and stimulating way.Online Resource Centre- Figures from the book available to download, to facilitate lecture slide preparation- Web link library of all URLs cited in the book, and hyperlinks to a wide range of further reading articles, to give students ready access to these resources - Links to PDB structures of all proteins cited in the book, to enable students to investigate the 3D structures of proteins in a visual, interactive way- Data from the book in computer-readable form, which is available for instant use to facilitate hands-on learning by the student- Guidance to help students answer problems from the text, to support and encourage self-learning

Table of contents provided by Syndetics

• Plan of the book (p. xix)
• 1 Introduction (p. 1)
• Life in space and time (p. 3)
• Evolution is the change over time in the world of living things (p. 4)
• Dogmas: central and peripheral (p. 6)
• Observables and data archives (p. 9)
• Information flow in bioinformatics (p. 12)
• Curation, annotation, and quality control (p. 13)
• The World Wide Web (p. 14)
• Electronic publication (p. 15)
• Computers and computer science (p. 16)
• Programming (p. 17)
• Biological classification and nomenclature (p. 21)
• Use of sequences to determine phylogenetic relationships (p. 24)
• Use of SINES and LINES to derive phylogenetic relationships (p. 30)
• Searching for similar sequences in databases: PSI-BLAST (p. 32)
• Introduction to protein structure (p. 40)
• The hierarchical nature of protein architecture (p. 41)
• Classification of protein structures (p. 44)
• Protein structure prediction and engineering (p. 51)
• Critical Assessment of Structure Prediction (CASP) (p. 52)
• Protein engineering (p. 52)
• Proteomics (p. 52)
• DNA microarrays (p. 53)
• Mass spectrometry (p. 54)
• Systems biology (p. 54)
• Clinical implications (p. 55)
• The future (p. 57)
• Recommended reading (p. 57)
• Exercises, Problems, and Weblems (p. 59)
• 2 Genome organization and evolution (p. 67)
• Genomes and proteomes (p. 68)
• Genes (p. 69)
• Proteomes (p. 71)
• Eavesdropping on the transmission of genetic information (p. 72)
• Mappings between the maps (p. 77)
• High-resolution maps (p. 78)
• Picking out genes in genomes (p. 80)
• Genomes of prokaryotes (p. 81)
• The genome of the bacterium Escherichia coli (p. 82)
• The genome of the archaeon Methanococcus jannaschii (p. 85)
• The genome of one of the simplest organisms: Mycoplasma genitalium (p. 86)
• Genomes of eukaryotes (p. 87)
• The genome of Saccharomyces cerevisiae (baker's yeast) (p. 89)
• The genome of Caenorhabditis elegans (p. 93)
• The genome of Drosophila melanogaster (p. 94)
• The genome of Arabidopsis thaliana (p. 95)
• The genome of Homo sapiens (the human genome) (p. 96)
• Protein coding genes (p. 97)
• Repeat sequences (p. 99)
• RNA (p. 100)
• Single-nucleotide polymorphisms (SNPs) (p. 101)
• Genetic diversity in anthropology (p. 102)
• Genetic diversity and personal identification (p. 103)
• Genetic analysis of cattle domestication (p. 104)
• Evolution of genomes (p. 104)
• Please pass the genes: horizontal gene transfer (p. 108)
• Comparative genomics of eukaryotes (p. 109)
• Recommended reading (p. 111)
• Exercises, Problems, and Weblems (p. 112)
• 3 Archives and information retrieval (p. 117)
• Introduction (p. 118)
• Database indexing and specification of search terms (p. 118)
• Follow-up questions (p. 120)
• Analysis of retrieved data (p. 121)
• The archives (p. 121)
• Nucleic acid sequence databases (p. 122)
• Genome databases (p. 124)
• Protein sequence databases (p. 124)
• Databases of structures (p. 128)
• Specialized, or 'boutique' databases (p. 135)
• Expression and proteomics databases (p. 136)
• Databases of metabolic pathways (p. 138)
• Bibliographic databases (p. 139)
• Surveys of molecular biology databases and servers (p. 139)
• Gateways to archives (p. 140)
• Access to databases in molecular biology (p. 141)
• Entrez (p. 141)
• The Sequence Retrieval System (SRS) (p. 148)
• The Protein Identification Resource (PIR) (p. 149)
• ExPASy-Expert Protein Analysis System (p. 150)
• Ensembl (p. 151)
• Where do we go from here? (p. 152)
• Recommended reading (p. 152)
• Exercises, Problems, and Weblems (p. 153)
• 4 Alignments and phylogenetic trees (p. 157)
• Introduction to sequence alignment (p. 158)
• The dotplot (p. 160)
• Dotplots and sequence alignments (p. 165)
• Measures of sequence similarity (p. 171)
• Scoring schemes (p. 171)
• Computing the alignment of two sequences (p. 175)
• Variations and generalizations (p. 175)
• Approximate methods for quick screening of databases (p. 176)
• The dynamic programming algorithm for optimal pairwise sequence alignment (p. 176)
• Significance of alignments (p. 182)
• Multiple sequence alignment (p. 186)
• Applications of multiple sequence alignments to database searching (p. 188)
• Profiles (p. 189)
• PSI-BLAST (p. 191)
• Hidden Markov Models (p. 193)
• Phylogeny (p. 198)
• Phylogenetic trees (p. 203)
• Clustering methods (p. 205)
• Cladistic methods (p. 206)
• The problem of varying rates of evolution (p. 207)
• Computational considerations (p. 208)
• Recommended reading (p. 209)
• Exercises, Problems, and Weblems (p. 210)
• 5 Protein structure and drug discovery (p. 219)
• Introduction (p. 220)
• Protein stability and folding (p. 223)
• The Sasisekharan-Ramakrishnan-Ramachandran plot describes allowed mainchain conformations (p. 223)
• The sidechains (p. 225)
• Protein stability and denaturation (p. 225)
• Protein folding (p. 228)
• Applications of hydrophobicity (p. 229)
• Superposition of structures, and structural alignments (p. 233)
• DALI (Distance-matrix ALIgnment) (p. 235)
• Evolution of protein structures (p. 236)
• Classifications of protein structures (p. 238)
• SCOP (p. 239)
• Protein structure prediction and modelling (p. 240)
• Critical Assessment of Structure Prediction (CASP) (p. 242)
• Secondary structure prediction (p. 244)
• Homology modelling (p. 250)
• Fold recognition (p. 252)
• Conformational energy calculations and molecular dynamics (p. 255)
• ROSETTA (p. 259)
• LINUS (p. 259)
• Assignment of protein structures to genomes (p. 263)
• Prediction of protein function (p. 265)
• Divergence of function: orthologues and paralogues (p. 266)
• Drug discovery and development (p. 269)
• The lead compound (p. 271)
• Bioinformatics in drug discovery and development (p. 273)
• Recommended reading (p. 284)
• Exercises, Problems, and Weblems (p. 285)
• 6 Proteomics and systems biology (p. 291)
• DNA microarrays (p. 293)
• Analysis of microarray data (p. 295)
• Mass spectrometry (p. 301)
• Identification of components of a complex mixture (p. 301)
• Protein sequencing by mass spectrometry (p. 304)
• Genome sequence analysis by mass spectrometry (p. 306)
• Systems biology (p. 311)
• Networks and graphs (p. 313)
• Network structure and dynamics (p. 318)
• Protein complexes and aggregates (p. 320)
• Properties of protein-protein complexes (p. 321)
• Protein interaction networks (p. 324)
• Regulatory networks (p. 329)
• Structures of regulatory networks (p. 330)
• Structural biology of regulatory networks (p. 336)
• Recommended reading (p. 339)
• Exercises, Problems, and Weblems (p. 339)
• Conclusions (p. 345)
• Answers to Exercises (p. 347)
• Glossary (p. 353)
• Index (p. 357)
• Colour plates

Author notes provided by Syndetics