Multiple sequence alignment methods
Author(s)
Bibliographic Information
Multiple sequence alignment methods
（Methods in molecular biology / John M. Walker, series editor, 1079）（Springer protocols）
Humana Press, c2014
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Note
Includes bibliographical references and index
"Humana Press is a brand of Springer"--T.p. verso
Description and Table of Contents
Description
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.
Table of Contents
Part I: Theory
1. Dynamic Programming
OE. Ufuk Nalbantoglu
2. Heuristic Alignment Methods
Osamu Gotoh
3. Objective Functions
Haluk Dogan and Hasan H. Otu
4. An Appraisal of Benchmarks for Multiple Sequence Alignment
Stefano Iantorno, Kevin Gori, Nick Goldman, Manuel Gil, and Christophe Dessimoz
5. BLAST and FASTA Similarity Searching for Multiple Sequence Alignment
William R. Pearson
Part II: Alignment Techniques
6. Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences
Fabian Sievers and Desmond G. Higgins
7. T-COFFEE: Tree-Based Consistency Objective Function for Alignment Evaluation
Cedrik Magis, Jean-Francois Taly, Giovanni Bussotti, Jia-Ming Chang, Paolo Di Tommaso, Ionas Erb, Jose Espinosa-Carrasco, and Cedric Notredame
8. MAFFT: Iterative Refinement and Additional Methods
Kazutaka Katoh and Daron M. Standley
9. Multiple Sequence Alignment Using Probcons and Probalign
Usman Roshan
10. Phylogeny-Aware Alignment with PRANK
Ari Loeytynoja
11. GramAlign: Fast Alignment Driven by Grammar-Based Phylogeny
David J. Russell
12. Multiple Sequence Alignment with DIALIGN
Burkhard Morgenstern
13. PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences
Sayed Mohammad Ebrahim Sahraeian, and Byung-Jun Yoon
14. Multiple Protein Sequence Alignment with MSAProbs
Yongchao Liu and Bertil Schmidt
15. Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATe
Kevin Liu and Tandy Warnow
16. PRALINE: A Versatile Multiple Sequence Alignment Toolkit
Punto Bawono and Jaap Heringa
17. PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and 3-Dimensional Structural Information
Jimin Pei and Nick V. Grishin
18. MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features
Xin Deng and Jianlin Cheng
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