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  • © 2014

Multiple Sequence Alignment Methods

Editors:

  • Presents a broad range of choices available for multiple sequence alignment generation
  • Focuses on practical aspects of algorithm usage
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1079)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xii
  2. Theory

    1. Front Matter

      Pages 1-1
    2. Dynamic Programming

      • Ö. Ufuk NalbantoÄŸlu
      Pages 3-27
    3. Heuristic Alignment Methods

      • Osamu Gotoh
      Pages 29-43
    4. Objective Functions

      • Haluk DoÄŸan, Hasan H. Otu
      Pages 45-58
    5. Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

      • Stefano Iantorno, Kevin Gori, Nick Goldman, Manuel Gil, Christophe Dessimoz
      Pages 59-73
  3. Alignment Techniques

    1. Front Matter

      Pages 103-103
    2. Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences

      • Fabian Sievers, Desmond G. Higgins
      Pages 105-116
    3. T-Coffee: Tree-Based Consistency Objective Function for Alignment Evaluation

      • Cedrik Magis, Jean-François Taly, Giovanni Bussotti, Jia-Ming Chang, Paolo Di Tommaso, Ionas Erb et al.
      Pages 117-129
    4. MAFFT: Iterative Refinement and Additional Methods

      • Kazutaka Katoh, Daron M. Standley
      Pages 131-146
    5. Phylogeny-aware alignment with PRANK

      • Ari Löytynoja
      Pages 155-170
    6. Multiple Sequence Alignment with DIALIGN

      • Burkhard Morgenstern
      Pages 191-202
    7. Multiple Protein Sequence Alignment with MSAProbs

      • Yongchao Liu, Bertil Schmidt
      Pages 211-218
    8. PRALINE: A Versatile Multiple Sequence Alignment Toolkit

      • Punto Bawono, Jaap Heringa
      Pages 245-262

About this book

From basic performing of sequence alignment through a proficiency at understanding how most industry-standard alignment algorithms achieve their results, Multiple Sequence Alignment Methods describes numerous algorithms and their nuances in chapters written by the experts who developed these algorithms.  The various multiple sequence alignment algorithms presented in this handbook give a flavor of the broad range of choices available for multiple sequence alignment generation, and their diversity is a clear reflection of the complexity of the multiple sequence alignment problem and the amount of information that can be obtained from multiple sequence alignments.  Each of these chapters not only describes the algorithm it covers but also presents instructions and tips on using their implementation, as is fitting with its inclusion in the highly successful Methods in Molecular Biology series.

 

Authoritative and practical, Multiple Sequence Alignment Methods provides a readily available resource which will allow practitioners to experiment with different algorithms and find the particular algorithm that is of most use in their application.

Editors and Affiliations

  • Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, USA

    David J Russell

Bibliographic Information

  • Book Title: Multiple Sequence Alignment Methods

  • Editors: David J Russell

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-646-7

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2014

  • Hardcover ISBN: 978-1-62703-645-0Published: 30 October 2013

  • Softcover ISBN: 978-1-4939-6047-7Published: 23 August 2016

  • eBook ISBN: 978-1-62703-646-7Published: 29 October 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 287

  • Number of Illustrations: 16 b/w illustrations, 47 illustrations in colour

  • Topics: Bioinformatics

Buy it now

Buying options

eBook USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access