Comparative genomics : empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families / edited by David Sankoff and Joseph H. Nadeau.

Format:

Book

Author/Creator:

Sankoff, David.

Contributor:

Nadeau, J. H. (Joseph H.)

Series:

Computational biology ; v. 1.

Computational biology ; v. 1

Language:

English

Subjects (All):

Genomes.

Gene mapping--Statistical methods.

Gene mapping.

Physiology, Comparative.

Genome.

Chromosome Mapping.

Statistics.

Medical Subjects:

Genome.

Chromosome Mapping.

Physiology, Comparative.

Physical Description:

xiii, 557 pages : illustrations ; 25 cm.

Place of Publication:

Boston, MA : Kluwer Academic, 2000.

Contents:

Comparative Genomics / David Sankoff, Joseph H. Nadeau 3

1. Mechanisms 9

Cytogenetics, Molecular Genetics, Population Genetics 11

Benefits of a Model of Segregation for the Understanding of Chromosomal Evolution / Thomas Faraut, Jacques Demongeot 13

Fixation of Chromosomal Rerrangements / Bryant F. McAllister 19

The Pathological Consequences and Evolutionary Implications of Recent Human Genomic Duplications / Christine O'Keefe, Evan Eichler 29

High Frequency of Inversions During Eukaryote Gene Order Evolution / Aoife McLysaght, Cathal Seoighe, Kenneth H. Wolfe 47

Human and Mouse DNA Sequence Comparisons: Further Evidence for a Mosaic Model of Genomic Evolution / Gord Brown, Duane Martindale, Michael D. Wilson, Ben F. Koop 59

Hot Spots in Chromosomal Breakage: From Description to Etiology / Jacques Demongeot, Juglio Aracena, Samia Ben Lamine, Marie-Ange Mermet, Olivier Cohen 71

2. Organelles: Mitochondria and Chloroplats 85

Rearrangements in Small Genomes 87

Chloroplast Gene Order and the Divergence of Plants and Algae, from the Normalized Number of Induced Breakpoints / David Sankoff, Melanie Deneault, David Bryant, Claude Lemieux, Monique Turmel 89

An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae / Mary E. Cosner, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, Stacia Wyman 99

Gene Order and Phylogenetic Information / Cyril Gallut, Veronique Barriel, Regine Vignes 123

The Duplication/Random Loss Model for Gene Rearrangement Exemplified by Mitochondrial Genomes of Deuterostome Animals / Jeffrey L. Boore 133

MAPIT

A Semi-Automated Approach to the Representation of Genetic Maps / Alexander Nip, Lin Liu, Charbel Seif, B. Franz Lang, Gertraud Burger 149

3. Combinatorial Algorithms 163

A New Set of Problems for a New Kind of Data 165

Experimental and Statistical Analysis of Sorting by Reversals / Alberto Caprara, Giuseppe Lancia 171

The Syntenic Diameter of the Space of N-Chromosome Genomes / Jon Kleinberg, David Liben-Nowell 185

Circular Permutations and Genome Shuffling / Vineet Bafna, Donald Beaver, Martin Furer, Pavel A. Pevzner 199

The Complexity of Calculating Exemplar Distances / David Bryant 207

An Alternative Algebraic Formalism for Genome Rearrangements / Joao Meidanis, Zanoni Dias 213

Approximation Algorithms for the Median Problem In the Breakpoint Model / Itsik Pe'er, Ron Shamir 225

Algorithms for Constructing Comparative Maps / Debra S. Goldberg, Susan McCouch, Jon Kleinberg 243

4. Prokaryotes 263

Genome Scrambling versus Functional Clustering 265

Dynamics of Gene Order Structures and Genomic Architectures / Siv G. E. Andersson, Kimmo Eriksson 267

Comparative Genome Analysis: Exploiting the Context of Genes to Infer Evolution and Predict Function / Peter Bork, Berend Snel, Gerrit Lehmann, Mikita Suyama, Thomas Dandekar, Warren Lathe III, Martijn Huynen 281

5. Statistics 295

The Quantification of Comparative Mapping 297

Accuracy and Robustness of Analyses Based on Numbers of Genes in Observed Segments / David Sankoff, Marie-Noelle Parent, David Bryant 299

Marker Density and Estimates of Chromosome Rearrangement / Daniel J. Schoen 307

Estimating the Number of Conserved Segments Between Species Using a Chromosome Based Model / David Waddington 321

CHROMTREE: Maximum Likelihood Estimation of Chromosomal Phylogenies / Jo Dicks 333

6. Nuclear Genomes 343

Evolutionary Inference from Comparative Mapping 345

Evolution of Karyotype Organisation in Accipitridae: a Translocation Model / Bertrand Bed'Hom 347

Syntenies of Unrelated Genes Conserved in Mammals and Nonvertebrates (A Review) / Zdenek Trachtulec, Jiri Forejt 357

Companion Animal Genetics / Leslie A. Lyons 367

The Essential Role of Comparative Maps in Livestock Genomics / James E. Womack 401

Comparative Genetics: From Hexaploid Wheat to Arabidopsis / Katrien M. Devos 411

Unraveling Crucifer Genomes Through Comparative Mapping / Isobel Parkin 425

Comparative Genomics of Plant Chromosomes / Andrew H. Paterson, John E. Bowers, Mark D. Burow, Xavier Draye, Christine G. Elsik, Chun-xiao Jiang, Catherine Susan Katsar, Tien-Hung Lan, Yann-Rong Lin, Reiguang Ming, Robert J. Wright 439

7. Gene and Genome Duplication and Multi-gene Families 459

How Can Duplication be Analyzed? 461

Recovery of Ancestral Tetraploids / Nadia El-Mabrouk 465

Genome Archaeology: Detecting Ancient Polyploidy in Contemporary Genomes / Todd J. Vision, Daniel G. Brown 479

Polyploidization and Vertebrate Origins: A Review of the Evidence / Austin L. Hughes 493

A Formal Model of Genomic DNA Multiplication and Amplification / Jerzy Tiuryn, Jan P. Radomski, Piotr P. Slonimski 503

A Simple Evolutionary Model for Genome Phylogeny Based on Gene Content / Xun Gu 515

GeneTree: A Tool for Exploring Gene Family Evolution / Roderic D. M. Page, James A. Cotton 525

Duplication, Rearrangement, and Reconciliation / David Sankoff, Nadia El-Mabrouk 537.

Notes:

Includes bibliographical references and index.

ISBN:

0792365836

OCLC:

50666952