『Multiple Sequence Alignment Methods』

目

David J. Russell (ed.)
（2014年刊行, Springer / Humana Press [Methods in Molecular Biology: 1079], New York, xii+287 pp., ISBN:9781627036450 [hbk] → 版元ページ）

【目次】
Preface (David J. Russell) v
Contributors xi

Part I: Theory

1. Dynamic Programming (Ö. Ufuk Nalbantoğlu) 3-27
2. Heuristic Alignment Methods (Osamu Gotoh) 29-43
3. Objective Functions (Doğan, Haluk and Hasan H. Otu) 45-58
4. Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment (Stefano Iantorno et al.) 59-73
5. BLAST and FASTA Similarity Searching for Multiple Sequence Alignment (William R. Pearson) 75-101

Part II: Alignment Techniques

6. Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences (Fabian Sievers and Desmond G. Higgins) 105-116
7. T-Coffee: Tree-Based Consistency Objective Function for Alignment Evaluation (Cedrik Magis et al.) 117-129
8. MAFFT: Iterative Refinement and Additional Methods (Kazutaka Katoh and Daron M. Standley) 131-146
9. Multiple Sequence Alignment Using Probcons and Probalign (Usman Roshan) 147-153
10. Phylogeny-aware alignment with PRANK (Ari Löytynoja) 155-170
11. GramAlign: Fast alignment driven by grammar-based phylogeny (David J. Russell) 171-189
12. Multiple Sequence Alignment with DIALIGN (Burkhard Morgenstern) 191-202
13. PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences (Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon) 203-210
14. Multiple Protein Sequence Alignment with MSAProbs (Yongchao Liu and Bertil Schmidt) 211-218
15. Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé (Kevin Liu and Tandy Warnow) 219-244
16. PRALINE: A Versatile Multiple Sequence Alignment Toolkit (Punto Bawono and Jaap Heringa) 245-262
17. PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information (Jimin Pei and Nick V. Grishin) 263-271
18. MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features (Xin Deng and Jianlin Cheng) 273-283


Index 285