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Full Description
This second edition provides updated and expanded chapters covering a broad sampling of useful and current methods in the rapidly developing and expanding field of bioinformatics. Bioinformatics, Volume I: Data, Sequence Analysis, and Evolution, Second Edition is comprised of three sections: Data and Databases, Sequence Analysis, and Phylogenetics and Evolution. The first section details bioinformatics methodologies in the generation of sequence and structural data and its organization into conceptual categories, and databases to facilitate further analyses. The Sequence Analysis section describes the fundamental methodologies for processing the sequences of biological molecules: techniques that are used in almost every pipeline of bioinformatics analysis, particularly in the preliminary stages of such pipelines. Last but not least, the phylogenetics and evolution section deals with methodologies that compare biological sequences for the purpose of understanding how they evolved. As a volume in the highly successful Methods in Molecular Biology series, chapters feature the kind of detail and expert implementation advice to ensure positive results.Comprehensive and practical, Bioinformatics, Volume I: Data, Sequence Analysis, and Evolution, Second Edition is an essential resource for graduate students, early career researchers, and others who are in the process of integrating new bioinformatics methods into their research.
Contents
Preface...Table of Contents...Contributing Authors...Part I Data and Databases1. Genome SequencingMansi Verma, Samarth Kulshreshtha, and Ayush Puri2. Sequence AssemblyXiaoqiu Huang3. A Practical Approach to Protein CrystallographyAndrea Ilari and Carmelinda Savino4. Managing Sequence DataChristopher O'Sullivan, Benjamin Busby, and Ilene Karsch Mizrachi5. Genome AnnotationImad Abugessaisa, Takeya Kasukawa, and Hideya Kawaji6. Working with OntologiesFrank Kramer and Tim Beissbarth7. The Classification of Protein DomainsNatalie L. Dawson, Ian Sillitoe, Russell L. Marsden, and Christine A. OrengoPart II Sequence Analysis8. Multiple Sequence AlignmentPunto Bawono, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, and Jaap Heringa9. Large-Scale Sequence ComparisonDevi Lal and Mansi Verma10. Genomic Database SearchingJames R. A. Hutchins11. Finding Genes in Genome SequenceAlice Carolyn McHardy and Andreas Kloetgen12. Sequence Segmentation with changeptGUIEdward Tasker and Jonathan M. KeithPart III Phylogenetics and Evolution13. Measuring Natural SelectionAnders Goncalves da Silva14. Inferring TreesSimon Whelan and David A. Morrison15. Identifying Optimal Models of EvolutionLars S. Jermiin, Vivek Jayaswal, Faisal M. Ababneh, and John Robinson16. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer EventsCheong Xin Chan, Robert G. Beiko, and Mark A. Ragan17. Detecting and Analyzing Genetic Recombination Using RDP4Darren P. Martin, Ben Murrell, Arjun Khoosal, and Brejnev Muhire18. Species Tree Estimation from Genome-Wide Data with GuenomuLeonardo de Oliveira Martins and David Posada
