Bioinformatics: Volume I: Data, Sequence Analysis and Evolution / Edition 1

Bioinformatics: Volume I: Data, Sequence Analysis and Evolution / Edition 1

by Jonathan M. Keith
     
 

Not only is the quantity of life science data expanding, but new types of biological data continue to be introduced as a result of technological development and a growing understanding of biological systems. Methods for analyzing these data are an increasingly important component of modern biological research. In Bioinformatics, leading researchers in the field

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Overview

Not only is the quantity of life science data expanding, but new types of biological data continue to be introduced as a result of technological development and a growing understanding of biological systems. Methods for analyzing these data are an increasingly important component of modern biological research. In Bioinformatics, leading researchers in the field provide a selection of the most useful and widely applicable methods, able to be applied as is, or with minor variations, to many specific problems. Volume I: Data, Sequence Analysis and Evolution examines a selection of methods involving the generation and organization of data, including sequence data, RNA and protein structures, microarray expression data and functional annotations, methods for discovering the functional components of genomes, whether they be genes, alternative splice sites, non-coding RNAs or regulatory motifs, and several of the most interesting methods in phylogenetics and evolution. As a volume of the highly successful Methods in Molecular Biology™ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.

Comprehensive and cutting-edge, Bioinformatics: Volume I: Data, Sequence Analysis and Evolution is an ideal reference for all scientists involved with the ever-growing array of data in the expanding field of life science.

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Product Details

ISBN-13:
9781588297075
Publisher:
Springer-Verlag New York, LLC
Publication date:
06/18/2008
Series:
Methods in Molecular Biology Series, #452
Edition description:
2008
Pages:
562
Product dimensions:
7.20(w) x 10.20(h) x 1.50(d)

Table of Contents

Table of Contents

Bioinformatics: Volume I: Data, Sequence Analysis and Evolution

Section I: Data and Databases

Chapter 1. Managing Sequence Data
Ilene Karsch Mizrachi

Chapter 2. RNA Structure Determination by NMR
Lincoln G. Scott and Mirko Hennig

Chapter 3. Protein Structure Determination by X-ray Crystallography
Andrea Ilari and Carmelinda Savino

Chapter 4. Pre-processing of Microarray Data and Analysis of Differential Expression
Steffen Durinck

Chapter 5. Developing an Ontology
Midori A. Harris

Chapter 6. Genome Annotation
Hideya Kawaji and Yoshihide Hayashizaki

Section II: Sequence Analysis

Chapter 7. Multiple Sequence Alignment
Walter Pirovano and Jaap Heringa

Chapter 8. Finding Genes in Genome Sequence
Alice Carolyn McHardy

Chapter 9. Bioinformatics Detection of Alternative Splicing
Namshin Kim and Christopher Lee

Chapter 10. Reconsruction of full-length isoforms from Splice Graphs
Yi Xing and Christopher Lee

Chapter 11. Sequence Segmentation
Jonathan Keith

Chapter 12. Discovering Sequence Motifs
Timothy L. Bailey

Section III: Phylogenetics and Evolution

Chapter 13. Modeling Sequence Evolution
Pietro Lio and Martin Bishop

Chapter 14. Inferring Trees
Simon Whelan

Chapter 15. Detecting the Presence and Location of Selection in Proteins
Tim Massingham

Chapter 16. Phylogenetic Model Evaluation
Lars Sommer Jermiin, Vivek Jayaswal, Faisal Ababneh and John Robinson

Chapter 17. Inferring Ancestral Gene Order
Julian M. Catchen, John S. Conery and John H. Postlethwait

Chapter 18. Genome Rearrangement by the Double Cut and Join Operation
Richard Friedberg, Aaron E. Darling and Sophia Yancopoulos

Chapter 19. Inferring Ancestral Protein Interaction Networks
Jose M. Peregrin-Alvarez

Chapter 20. Computational Tools for the Analysis of Rearrangements in Mammalian Genomes
Guillaume Bourque and Glenn Tesler

Chapter 21. Detecting Lateral Genetic Transfer: a Phylogenetic Approach
Robert G. Beiko and Mark A. Ragan

Chapter 22. Detecting Genetic Recombination
Georg F. Weiller

Chapter 23. Inferring patterns of migration
Paul M.E. Bunje and Thierry Wirth

Chapter 24. Fixed-Parameter Algorithms in Phylogenetics
Jens Gramm, Arfst Nickelsen and Till Tantau

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