Sequence Alignment : Methods, Models, Concepts, and Strategies

The sequencing of the human genome involved thousands of scientists but used relatively few tools. Today, obtaining sequences is simpler, but aligning the sequences--making sure that sequences from one source are properly compared to those from other sources--remains a complicated but underappreciated aspect of comparative molecular biology. This volume, the first to focus on this crucial step in analyzing sequence data, is about the practice of alignment, the procedures by which alignments are established, and more importantly, how the outcomes of any alignment algorithm should be interpreted. Edited by Michael S. Rosenberg with essays by many of the field's leading experts, Sequence Alignment covers molecular causes, computational advances, approaches for assessing alignment quality, and philosophical underpinnings of the algorithms themselves. Table of Contents......Page 6 Contributors......Page 8 Preface......Page 12 1. Sequence Alignment......Page 18 2. Insertion and Deletion Events, Their Molecular Mechanisms, and Their Impact on Sequence Alignments......Page 40 3. Local versus Global Alignments......Page 56 4. Computing Multiple Sequence Alignment with Template-Based Methods......Page 72 5. Sequence Evolution Models for Simultaneous Alignment and Phylogeny Reconstruction......Page 88 6. Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment......Page 112 7. Structural and Evolutionary Considerations for Multiple Sequence Alignment of RNA, and the Challenges for Algorithms That Ignore Them......Page 122 8. Constructing Alignment Benchmarks......Page 168 9. Simulation Approaches to Evaluating Alignment Error and Methods for Comparing Alternate Alignments......Page 196 10. Robust Inferences from Ambiguous Alignments......Page 226 11. Strategies for Efficient Exploitation of the Informational Content of Protein Multiple Alignments......Page 288 References......Page 314 Index......Page 350

sequence Alignment Represents The Final Frontier In The Development Of Repeatable, Comprehensive Methods For Phylogenetic Analysis. This Book Will Inform Readers About The Current Status Of Alignment Methods And Will Help Stimulate Additional Work In The Field.—david M. Hillis, University Of Texas

sequence Alignment provides An In-depth Treatment Of The Prerequisite To Many Evolutionary Analyses By Presenting A Diversity Of Opinions On The Best Way To Align Complex Molecular Sequence Data. Topics Covered Include The Basic Algorithms Used, Global Versus Local Procedures, The Robustness Alignment Error Detection, And A Description Of The Programs Now Available. sequence Alignment is A Reassuring Companion, Guiding The Reader Through A Large And Complicated Field.—john Huelsenbeck, Department Of
integrative Biology, University Of California, Berkeley

Sequence alignment : concepts and history Insertion and deletion events, their molecular mechanisms, and their impact on sequence alignments Local versus global alignments Computing multiple sequence alignment with template based methods Sequence evolution models for simultaneous alignment and phylogeny reconstruction Phylogenetic hypotheses and the utility of multiple sequence alignment Structural and evolutionary considerations for multiple sequence alignment of RNA, and the challenges for algorithms that ignore them Constructing alignment benchmarks Simulation approaches to evaluating alignment error and methods for comparing alternate alignments Robust inferences from ambiguous alignments Strategies for efficient exploitation of the informational content of protein multiple alignments. "The sequencing of the human genome involved thousands of scientists but used relatively few tools. Today, obtaining sequences is simpler, but aligning the sequences - making sure that sequences from one source are properly compared to those from other sources - remains a complicated but underappreciated aspects of comparative molecular biology. This volume is about the practice of alignment, the procedures by which alignments are established, and, more importantly, how the outcomes of any alignment algorithm should be interpreted."--Jacket