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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.

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Preface...
Table of Contents...
Contributing Authors...

Part I Data and Databases

1. Genome Sequencing
Mansi Verma, Samarth Kulshreshtha, and Ayush Puri

2. Sequence Assembly
Xiaoqiu Huang

3. A Practical Approach to Protein Crystallography
Andrea Ilari and Carmelinda Savino

4. Managing Sequence Data
Christopher O´Sullivan, Benjamin Busby, and Ilene Karsch Mizrachi

5. Genome Annotation
Imad Abugessaisa, Takeya Kasukawa, and Hideya Kawaji

6. Working with Ontologies
Frank Kramer and Tim Beißbarth

7. The Classification of Protein Domains
Natalie L. Dawson, Ian Sillitoe, Russell L. Marsden, and Christine A. Orengo

Part II Sequence Analysis

8. Multiple Sequence Alignment
Punto Bawono, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, and Jaap Heringa

9. Large-Scale Sequence Comparison
Devi Lal and Mansi Verma

10. Genomic Database Searching
James R. A. Hutchins

11. Finding Genes in Genome Sequence
Alice Carolyn McHardy and Andreas Kloetgen

12. Sequence Segmentation with changeptGUI
Edward Tasker and Jonathan M. Keith

Part III Phylogenetics and Evolution

13. Measuring Natural Selection
Anders Gon‡alves da Silva

14. Inferring Trees
Simon Whelan and David A. Morrison

15. Identifying Optimal Models of Evolution
Lars S. Jermiin, Vivek Jayaswal, Faisal M. Ababneh, and John Robinson

16. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events
Cheong Xin Chan, Robert G. Beiko, and Mark A. Ragan

17. Detecting and Analyzing Genetic Recombination Using RDP4
Darren P. Martin, Ben Murrell, Arjun Khoosal, and Brejnev Muhire

18. Species Tree Estimation from Genome-Wide Data with Guenomu
Leonardo de Oliveira Martins and David Posada

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