Bioinformatics

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 Goncalves 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