Multiple Sequence Alignment: Methods and Protocols

ISBN-13: 9781071610350 / Angielski / Twarda / 2020 / 321 str.

Kazutaka Katoh

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Basic Tools for Computing MSAa

1. The Clustal Omega Multiple Alignment Package

Fabian Sievers and Desmond G. Higgins

2. Phylogeny-Aware Alignment with PRANK and PAGAN

Ari Löytynoja

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

Jorge González-Domínguez

Part II Tools for Specific MSA Problems

Handling DNA/Protein Sequences Simultaneously

4. Aligning Protein-Coding Nucleotide Sequences with MACSE

Vincent Ranwez, Nathalie Chantret, and Frédéric Delsuc

5. Cooperation of Spalm and Prrn5 for Construction of Gene-Structure-Aware Multiple Sequence Alignment

Osamu Gotoh

Large Number of Sequences

6. Multiple Sequence Alignment Computation using the T-Coffee Regressive Algorithm Implementation

Edgar Garriga, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Evan Floden, and Cedric Notredame

7. Multiple Sequence Alignment for Large Heterogeneous Datasets using SATé, PASTA, and UPP

Tandy Warnow and Siavash Mirarab

8. Sequence Comparison without Alignment: The SpaM Approaches

Burkhard Morgenstern

Unreliable Data

9. Lamassemble: Multiple Alignment and Consensus Sequence of Long Reads

Martin C. Frith, Satomi Mitsuhashi, and Kazutaka Katoh

10. Automated Removal of Non-Homologous Sequence Stretches with PREQUAL

Iker Irisarri, Fabien Burki, and Simon Whelan

Protein Structures

11. Analysis of Protein Intermolecular Interaction with MAFFT-DASH

John Rozewicki, Songling Li, Kazutaka Katoh, and Daron M. Standley

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

Dmitry Suplatov, Yana Sharapova, and Vytas Švedas

Part III Visualization

13. Alignment of Biological Sequences with Jalview

James B. Procter, G. Mungo Carstairs, Ben Soares, Kira Mourão, T. Charles Ofoegbu, Daniel Barton, Lauren Lui, Anne Menard, Natasha Sherstnev, David Roland-Martinez, Suzanne Duce, David M.A. Martin, and Geoffrey J. Marton

14. Evolutionary Sequence Analysis and Visualization with Wasabi

Andres Veidenberg and Ari Löytynoja

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

Manolo Gouy, Eric Tannier, Nicolas Comte, and David Parsons

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

Anatoliy Kuznetsov and Colleen J. Bollin

Part IV Open Problems

17. Revisiting Evaluation of Multiple Sequence Alignment Methods

Tandy Warnow

Subject Index List…

Blurb

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