Multiple sequence alignment methods

Author(s)

• Russell, David James

Bibliographic Information

Multiple sequence alignment methods

edited by David J. Russell

（Methods in molecular biology / John M. Walker, series editor, 1079）（Springer protocols）

Humana Press, c2014

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

by "Nielsen BookData"

• NCID: BB20767404
• ISBN:
  • 9781627036450
  • 1627036458
• LCCN: 2013947475
• Country Code: us
• Title Language Code: eng
• Text Language Code: eng
• Place of Publication: New York
• Pages/Volumes: xii, 287 p.
• Size: 26 cm
• Classification:
  • LCC : QH324.2
  • NLM : W1
  • NLM : QU 39
• Subject Headings:
  • LCSH : Sequence alignment (Bioinformatics) -- Laboratory manuals
  • LCSH : Computational biology -- Laboratory manuals
  • MESH : Computational Biology -- methods -- Handbooks
  • MESH : Sequence Alignment -- methods -- Handbooks
  • MESH : Databases, Protein -- Handbooks
• Parent Bibliography ID:
  • BA10794673
  • BA88873632