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Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition


Description: Reviews of the Second Edition "In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt." --Eric Lander, from the Foreword to the Second Edition "The editors and the chapter authors of this book are to be applauded for providing biologists with lucid and comprehensive descriptions of essential topics in bioinformatics. This book is easy to read, highly informative, and certainly timely. It is most highly recommended for students and for established investigators alike, for anyone who needs to know how to access and use the information derived in and from genomic sequencing projects." --Trends in Genetics "It is an excellent general bioinformatics text and reference, perhaps even the best currently available . . . Congratulations to the authors, editors, and publisher for producing a weighty, authoritative, readable, and attractive book." --Briefings in Bioinformatics "This book, written by the top scientists in the field of bioinformatics, is the perfect choice for every molecular biology laboratory." --The Quarterly Review of Biology This fully revised version of a world-renowned bestseller provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. Using relevant biological examples, the book provides background on and strategies for using many of the most powerful and commonly used computational approaches for biological discovery. This Third Edition reinforces key concepts that have stood the test of time while making the reader aware of new and important developments in this fast-moving field. With a new full-color and enlarged page design, Bioinformatics, Third Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists. This new edition features: New chapters on genomic databases, predictive methods using RNA sequences, sequence polymorphisms, protein structure prediction, intermolecular interactions, and proteomic approaches for protein identification Detailed worked examples illustrating the strategic use of the concepts presented in each chapter, along with a collection of expanded,more rigorous problem sets suitable for classroom use Special topic boxes and appendices highlighting experimental strategies and advanced concepts Annotated reference lists, comprehensive lists of relevant Web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics Bioinformatics, Third Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, clinical research, proteomics, and computational biology.


Contents: Foreword (Lee Hood). Preface. Contributors. PART ONE: BIOLOGICAL DATABASES. 1. Sequence Databases (Rolf Apweiler). 2. Mapping Databases (Peter S. White and Tara C. Matise). 3. Information Retrieval from Biological Databases (Andreas D. Baxevanis). 4. Genomic Databases (Tyra G. Wolfsberg). PART TWO: ANALYSIS AT THE NUCLEOTIDE LEVEL. 5. Predictive Methods Using DNA Sequences (Enrique Blanco and Roderic Guigó). 6. Predictive Methods Using RNA Sequences (David Mathews and Michael Zuker). 7. Sequence Polymorphisms (James C. Mullikin and Stephen T. Sherry). PART THREE: ANALYSIS AT THE PROTEIN LEVEL. 8. Predictive Methods Using Protein Sequences (Yanay Ofran and Burkhard Rost). 9. Protein Structure Prediction and Analysis (David Wishart). 10. Intermolecular Interactions and Biological Pathways (Gary D. Bader and Anton J. Enright). PART FOUR: INFERRING RELATIONSHIPS. 11. Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis). 12. Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton). 13. Sequence Assembly and Finishing Methods (Nancy F. Hansen, Pamela Jacques Thomas and Gerard G. Bouffard). 14. Phylogenetic Analysis (Fiona S. L. Brinkman). 15. Computational Approaches in Comparative Genomics (Andreas D. Baxevanis). 16. Using DNA Microarrays to Assay Gene Expression (John Quackenbush). 17. Proteomics and Protein Identification (Mark R. Holmes, Kevin R. Ramkissoon and Morgan C. Giddings). PART FIVE: DEVELOPING TOOLS. 18. Using Perl to Facilitate Biological Analysis (Lincoln D. Stein). Appendices. Glossary. Index. .


Summary: This fully revised Third Edition to an already classic resource provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. With a new full-color, enlarged page design, this edition offers the most readable, up-to-date, and thorough introduction to the field for biologists. All new features include special boxes, enhanced use of real examples, and expanded problem sets with answers provided on the books dedicated website. A glossary and appendix of sample file formats rounds out the books reader-friendly, hands-on treatment. The chapters have been reorganized into a more logical flow, with five main sections and a concluding section offering a primer on the use of Perl. Following the editors introduction and perspective on why bioinformatics is important, the first two sections cover database structure and content, with new chapters on genome annotation and genomic databases. The next two sections discuss nucleotide and protein analysis, including new chapters on predictive methods using RNA sequences, protein structure prediction, and protein-protein interactions. The fifth section then deals comprehensively with inferring relationships, from sequence alignment to microarray analysis.




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