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Bioinformatics

Volume I: Data, Sequence Analysis, and Evolution

  • Book
  • © 2017

Overview

Editors:
  1. Jonathan M. Keith

    1. Monash University, Melbourne, Australia

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1525)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-x
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  2. Data and Databases

    1. Front Matter

      Pages 1-1
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    2. Genome Sequencing

      • Mansi Verma, Samarth Kulshrestha, Ayush Puri
      Pages 3-33

    3. Sequence Assembly

      • Xiaoqiu Huang
      Pages 35-45

    4. A Practical Approach to Protein Crystallography

      • Andrea Ilari, Carmelinda Savino
      Pages 47-78

    5. Managing Sequence Data

      • Christopher O’Sullivan, Benjamin Busby, Ilene Karsch Mizrachi
      Pages 79-106

    6. Genome Annotation

      • Imad Abugessaisa, Takeya Kasukawa, Hideya Kawaji
      Pages 107-121

    7. Working with Ontologies

      • Frank Kramer, Tim Beißbarth
      Pages 123-135

    8. The Classification of Protein Domains

      • Natalie Dawson, Ian Sillitoe, Russell L. Marsden, Christine A. Orengo
      Pages 137-164

  3. Sequence Analysis

    1. Front Matter

      Pages 165-165
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    2. Multiple Sequence Alignment

      • Punto Bawono, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, Jaap Heringa
      Pages 167-189

    3. Large-Scale Sequence Comparison

      • Devi Lal, Mansi Verma
      Pages 191-224

    4. Genomic Database Searching

      • James R. A. Hutchins
      Pages 225-269

    5. Finding Genes in Genome Sequence

      • Alice Carolyn McHardy, Andreas Kloetgen
      Pages 271-291

    6. Sequence Segmentation with changeptGUI

      • Edward Tasker, Jonathan M. Keith
      Pages 293-312

  4. Phylogenetics and Evolution

    1. Front Matter

      Pages 313-313
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    2. Measuring Natural Selection

      • Anders Gonçalves da Silva
      Pages 315-347

    3. Inferring Trees

      • Simon Whelan, David A. Morrison
      Pages 349-377

    4. Identifying Optimal Models of Evolution

      • Lars S. Jermiin, Vivek Jayaswal, Faisal M. Ababneh, John Robinson
      Pages 379-420

    5. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events

      • Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan
      Pages 421-432
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Keywords

About this book

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.

Editors and Affiliations

  • Monash University, Melbourne, Australia

    Jonathan M. Keith

Bibliographic Information

  • Book Title: Bioinformatics

  • Book Subtitle: Volume I: Data, Sequence Analysis, and Evolution

  • Editors: Jonathan M. Keith

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6622-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2017

  • Hardcover ISBN: 978-1-4939-6620-2Published: 29 November 2016

  • Softcover ISBN: 978-1-4939-8252-3Published: 21 June 2018

  • eBook ISBN: 978-1-4939-6622-6Published: 26 November 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 491

  • Number of Illustrations: 36 b/w illustrations, 81 illustrations in colour

  • Topics: Bioinformatics

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