| Description |
xvi, 371 pages : illustrations (some color) ; 27 cm |
| Contents |
Contents note continued: Analysis and processing of retrieved data -- The archives -- Nucleic acid sequence databases -- Genome databases and genome browsers -- Protein sequence databases -- Databases of protein families -- Databases of structures -- Classifications of protein structures -- Accuracy and precision of protein structure determinations -- Specialized, or ̀boutique', databases -- Expression and proteomics databases -- Bibliographic databases -- Surveys of molecular biology databases and servers -- Gateways to archives -- Access to databases in molecular biology -- ENTREZ -- The Protein Identification Resource -- ExPASy: Expert Protein Analysis System -- Where do we go from here? -- Recommended reading -- Exercises and problems -- 5.Alignments and phylogenetic trees -- Introduction to sequence alignment -- The dotplot -- Dotplots and sequence alignments -- Measures of sequence similarity -- Scoring schemes -- |
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Contents note continued: Bioinformatics in drug discovery and development -- Molecular modelling in drug discovery -- Recommended reading -- Exercises and problems -- 7.Introduction to systems biology -- Introduction -- Networks and graphs -- Connectivity in networks -- Dynamics, stability, and robustness -- Some sources of ideas for systems biology -- Complexity of sequences -- Computational complexity -- Static and dynamic complexity -- Chaos and predictability -- Recommended reading -- Exercises and problems -- 8.Metabolic pathways -- Classification and assignment of protein function -- The Enzyme Commission -- The Gene Ontology Consortium protein function classification -- Catalysis by enzymes -- Active sites -- Cofactors -- Protein---ligand binding equilibria -- Enzyme kinetics -- Measures of effectiveness of enzymes -- How do proteins evolve new functions? -- Control over enzyme activity -- Structural mechanisms of evolution of altered or novel protein functions -- |
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Contents note continued: Critical Assessment of Structure Prediction -- Protein engineering -- Proteomics and transcriptomics -- DNA microarrays -- Transcriptomics and RNA sequencing -- Mass spectrometry -- Systems biology -- Clinical implications -- The future -- Recommended reading -- Exercises and problems -- 2.Genome organization and evolution -- Genomes, transcriptomes, and proteomes -- Genes -- Proteomics and transcriptomics -- Eavesdropping on the transmission of genetic information -- Identification of genes associated with Inherited diseases -- Mappings between the maps -- High resolution maps -- Genome-wide association studies -- Picking out genes in genomes -- Genome-sequencing projects -- Genomes of prokaryotes -- The genome of the bacterium Escherichia coli -- The genome of the archaeon Methanococcus jannaschii -- The genome of one of the simplest organisms: Mycoplasma genitalium -- Metagenomics: the collection of genomes in a coherent environmental sample -- |
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Contents note continued: Derivation of substitution matrices: PAM and BLOSUM matrices -- Computing the alignment of two sequences -- Variations and generalizations -- Approximate methods for quick screening of databases -- The dynamic-programming algorithm for optimal pairwise sequence alignment -- Significance of alignments -- Multiple sequence alignment -- Applications of multiple sequence alignments and database searching -- Profiles -- PSI-BLAST -- Hidden Markov models -- Phylogeny -- Determination of taxonomic relationships from molecular properties -- Phylogenetic trees -- Clustering methods -- Cladistic methods -- Reconstruction of ancestral sequences -- The problem of varying rates of evolution -- Are trees the correct way to present phylogenetic relationships? -- Computational considerations -- Putting it all together -- Recommended reading -- Exercises and problems -- 6.Structural bioinformatics and drug discovery -- Introduction -- Protein stability and folding -- |
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Contents note continued: Properties of protein---protein complexes -- Protein interaction networks -- Regulatory networks -- Signal transduction and transcriptional control -- Structures of regulatory networks -- Structural biology of regulatory networks -- The genetic switch of bacteriophage λ -- What are the characteristics of the switch that must be implemented by DNA---protein interactions? -- The materials -- How to ̀throw' the switch -- The genetic regulatory network of Saccharomyces cerevisiae -- Adaptability of the yeast regulatory network -- Recommended reading -- Exercises and problems |
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Contents note continued: Protein evolution at the level of domain assembly -- Databases of metabolic pathways -- EcoCyc -- The Kyoto Encyclopedia of Genes and Genomes -- Evolution and phylogeny of metabolic pathways -- Pathway comparison -- Alignment of metabolic pathways -- Comparing linear metabolic pathways -- Comparing nonlinear metabolic pathways: the pentose phosphate pathway and the Calvin-Benson cycle -- Dynamics of metabolic networks -- Robustness of metabolic networks -- Dynamic modelling of metabolism -- Recommended reading -- Exercises and problems -- 9.Gene expression and regulation -- DNA microarrays -- Microarray data are quantitative but imprecise -- Analysis of microarray data -- Mass spectrometry -- Identification of components of a complex mixture -- Protein sequencing by mass spectrometry -- Measuring deuterium exchange in proteins -- Genome sequence analysis by mass spectrometry -- Protein complexes and aggregates -- |
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Contents note continued: The Public Library of Science -- Traditional and digital libraries -- How to populate a digital library -- The information explosion -- The web: higher dimensions -- New media: video, sound -- Searching the literature -- Bibliography management -- Databases -- Database contents -- The literature as a database -- Database organization -- Annotation -- Database quality control -- Database access -- Links -- Database interoperability -- Data mining -- Programming languages and tools -- Traditional programming languages -- Scripting languages -- Program libraries specialized for molecular biology -- Java: computing over the web -- Markup languages -- Natural language processing -- Natural language processing and mining the biomedical literature -- Applications of text mining -- Recommended reading -- Exercises and problems -- 4.Archives and information retrieval -- Database indexing and specification of search terms -- Follow-up questions -- |
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Contents note continued: The Sasisekharan---Ramakrishnan---Ramachandran plot describes allowed mainchain conformations -- The sidechains -- Protein stability and denaturation -- Protein folding -- Applications of hydrophobicity -- Coiled-coiled proteins -- Superposition of structures, and structural alignments -- DALI and MUSTANG -- Evolution of protein structures -- Classifications of protein structures -- Protein structure prediction and modelling -- A priori and empirical methods -- Critical Assessment of Structure Prediction -- Secondary structure prediction -- Homology modelling -- Fold recognition -- Conformational energy calculations and molecular dynamics -- Assignment of protein structures to genomes -- Prediction of protein function -- Divergence of function: orthologues and paralogues -- Drug discovery and development -- The lead compound -- Improving on the lead compound: quantitative structure-activity relationships -- |
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Contents note continued: The human microbiome -- Genomes of eukarya -- Gene families -- The genome of Saccharomyces cerevisiae (baker's yeast) -- The genome of Caenorhabditis elegans -- The genome of Drosophila melanogaster -- The genome of Arabidopsis thaliana -- The genome of Homo sapiens (the human genome) -- Protein-coding genes -- Repeat sequences -- RNA -- Single-nucleotide polymorphisms and haplotypes -- Systematic measurements and collections of single-nucleotide polymorphisms -- Ethical, legal, and social issues -- Genetic diversity in anthropology -- DNA sequences and languages -- Genetic diversity and personal identification -- Evolution of genomes -- Please pass the genes: horizontal gene transfer -- Comparative genomics of eukarya -- Recommended Reading -- Exercises and problems -- 3.Scientific publications and archives: media, content, and access -- The scientific literature -- Economic factors governing access to schoiarly publications -- Open access -- |
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Machine generated contents note: 1.Introduction -- Life in space and time -- Phenotype = genotype + environment + life history + epigenetics -- Evolution is the change over time in the world of living things -- Dogmas: central and peripheral -- Statics and dynamics -- Networks -- Observables and data archives -- A database without effective modes of access is merely a data graveyard -- Information flow In bioinformatics -- Curation, annotation, and quality control -- The world-wide web -- Electronic publication -- Computers and computer science -- Programming -- Biological classification and nomenclature -- Use of sequences to determine phylogenetic relationships -- Use of SINES and LINES to derive phylogenetic relationships -- Searching for similar sequences in databases: PSI-BLAST -- Introduction to protein structure -- The hierarchical nature of protein architecture -- Classification of protein structures -- Protein structure prediction and engineering -- |
| Summary |
Fully revised and updated, the fourth edition of Introduction to Bioinformatics shows how bioinformatics can be used as a powerful set of tools for retrieving and analyzing this biological data, and how bioinformatics can be applied to a wide range of disciplines such as molecular biology, medicine, biotechnology, forensic science, and anthropology. This new edition contains two new chapters, with significantly increased coverage of metabolic pathways, and gene expression and regulation. Written for students without a detailed prior knowledge of programming, this book is the perfect introduction to the field of bioinformatics, providing friendly guidance and advice on how to use various methods and techniques. Additionally, frequent examples, self-test questions, problems, and exercises are incorporated throughout the text to encourage self-directed learning |
| Notes |
Previous edition: 2008 |
| Bibliography |
Includes bibliographical references and index |
| Subject |
Bioinformatics.
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Computational biology.
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Computational Biology.
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| LC no. |
2013372147 |
| ISBN |
9780199651566 (paperback) |
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