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Multiple Sequence Alignment

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Kazutaka Katoh

    1. Research Institute for Microbial Disease, Osaka University, Osaka, Japan

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2231)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Basic Tools for Computing MSAa

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. The Clustal Omega Multiple Alignment Package

      • Fabian Sievers, Desmond G. Higgins
      Pages 3-16

    3. Phylogeny-Aware Alignment with PRANK and PAGAN

      • Ari Löytynoja
      Pages 17-37

    4. Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI

      • Jorge González-Domínguez
      Pages 39-47

  3. Tools for Specific MSA Problems

    1. Front Matter

      Pages 49-49
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    2. Aligning Protein-Coding Nucleotide Sequences with MACSE

      • Vincent Ranwez, Nathalie Chantret, Frédéric Delsuc
      Pages 51-70

    3. Cooperation of Spaln and Prrn5 for Construction of Gene-Structure-Aware Multiple Sequence Alignment

      • Osamu Gotoh
      Pages 71-88

    4. Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation

      • Edgar Garriga, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis et al.
      Pages 89-97

    5. Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP

      • Tandy Warnow, Siavash Mirarab
      Pages 99-119

    6. Sequence Comparison Without Alignment: The SpaM Approaches

      • Burkhard Morgenstern
      Pages 121-134

    7. lamassemble: Multiple Alignment and Consensus Sequence of Long Reads

      • Martin C. Frith, Satomi Mitsuhashi, Kazutaka Katoh
      Pages 135-145

    8. Automated Removal of Non-homologous Sequence Stretches with PREQUAL

      • Iker Irisarri, Fabien Burki, Simon Whelan
      Pages 147-162

    9. Analysis of Protein Intermolecular Interactions with MAFFT-DASH

      • John Rozewicki, Songling Li, Kazutaka Katoh, Daron M. Standley
      Pages 163-177

    10. Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies

      • Dmitry Suplatov, Yana Sharapova, Vytas Švedas
      Pages 179-200

  4. Visualization

    1. Front Matter

      Pages 201-201
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    2. Alignment of Biological Sequences with Jalview

      • James B. Procter, G. Mungo Carstairs, Ben Soares, Kira Mourão, T. Charles Ofoegbu, Daniel Barton et al.
      Pages 203-224Open Access

    3. Evolutionary Sequence Analysis and Visualization with Wasabi

      • Andres Veidenberg, Ari Löytynoja
      Pages 225-240

    4. Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

      • Manolo Gouy, Eric Tannier, Nicolas Comte, David P. Parsons
      Pages 241-260

    5. NCBI Genome Workbench: Desktop Software for Comparative Genomics, Visualization, and GenBank Data Submission

      • Anatoliy Kuznetsov, Colleen J. Bollin
      Pages 261-295
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Keywords

About this book

Chapter “Alignment of Biological Sequences with Jalview” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Editors and Affiliations

  • Research Institute for Microbial Disease, Osaka University, Osaka, Japan

    Kazutaka Katoh

Bibliographic Information

  • Book Title: Multiple Sequence Alignment

  • Book Subtitle: Methods and Protocols

  • Editors: Kazutaka Katoh

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1036-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1035-0Published: 09 December 2020

  • Softcover ISBN: 978-1-0716-1038-1Published: 09 December 2020

  • eBook ISBN: 978-1-0716-1036-7Published: 08 December 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 321

  • Number of Illustrations: 22 b/w illustrations, 90 illustrations in colour

  • Topics: Bioinformatics

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