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.

Part I: Theory

1. Dynamic Programming

            Ö. 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-François Taly, Giovanni Bussotti, Jia-Ming Chang, Paolo Di Tommaso, Ionas Erb, José 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 Löytynoja

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 SATé

            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