Multiple Sequence Alignment Methods (e-book) (used book) | bookbook.eu

Description

Part I: Theory

1. Dynamic Programming

Ö. Ufuk Nalbantoğlu

2. Heuristic Alignment Methods

Osamu Gotoh

3. Objective Functions

Haluk Doğan 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