Comparative Genomics: RECOMB 2005 International Workshop, RCG 2005, Dublin, Ireland, September 18-20, 2005, Proceedings (Lecture Notes in Computer Science, 3678)

This book constitutes the refereed proceedings of the RECOMB 2005 Satellite Workshop, the 3rd RECOMB Comparative Genomics meeting RCG 2005, held in Dublin, Ireland in September 2005. The 14 revised full papers presented were carefully reviewed and selected from 21 initial submissions. The papers address a broad variety of aspects and components of the field of comparative genomics, ranging from new quantitative discoveries about genome structure and process to theorems on the complexity of computational problems inspired by genome comparison. Lower Bounds For Maximum Parsimony With Gene Order Data / Abraham Bachrach, Kevin Chen, Chris Harrelson, Radu Mihaescu, Satish Rao And Apurva Shah -- Genes Order And Phylogenetic Reconstruction : Application To [gamma]-proteobacteria / Guillaume Blin, Cedric Chauve And Guillaume Fertin -- Maximizing Synteny Blocks To Identify Ancestral Homologs / Guillaume Bourque, Yasmine Yacef And Nadia El-mabrouk -- An Expectation-maximization Algorithm For Analysis Of Evolution Of Exon-intron Structure Of Eukaryotic Genes / Liran Carmel, Igor B. Rogozin, Yuri I. Wolf And Eugene V. Koonin -- Likely Scenarios Of Intron Evolution / Miklos Csuros -- Oma, A Comprehensive, Automated Project For The Identification Of Orthologs From Complete Genome Data : Introduction And First Achievements / Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider And Gaston H. Gonnet -- The Incompatible Desiderata Of Gene Cluster Properties / Rose Hoberman And Dannie Durand -- The String Barcoding Problem Is Np-hard / Marcello Dalpasso, Giuseppe Lancia And Romeo Rizzi -- A Partial Solution To The C-value Paradox / Jeffrey M. Marcus -- Individual Gene Cluster Statistics In Noisy Maps / Narayanan Raghupathy And Dannie Durand -- Power Boosts For Cluster Tests / David Sankoff And Lani Haque -- Reversals Of Fortune / David Sankoff, Chungfang Zheng And Aleksander Lenert -- Very Low Power To Detect Asymmetric Divergence Of Duplicated Genes / Cathal Seoighe And Konrad Scheffler -- A Framework For Orthology Assignment From Gene Rearrangement Data / Krister M. Swenson, Nicholas D. Pattengale And Bernard M. E. Moret. Aoife Mclysaght, Daniel H. Huson (eds.). Includes Bibliographical References And Index. Also Issued Online. Front Matter....Pages - Lower Bounds for Maximum Parsimony with Gene Order Data....Pages 1-10 Genes Order and Phylogenetic Reconstruction: Application to γ -Proteobacteria....Pages 11-20 Maximizing Synteny Blocks to Identify Ancestral Homologs....Pages 21-34 An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes....Pages 35-46 Likely Scenarios of Intron Evolution....Pages 47-60 OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements....Pages 61-72 The Incompatible Desiderata of Gene Cluster Properties....Pages 73-87 The String Barcoding Problem is NP-Hard....Pages 88-96 A Partial Solution to the C-Value Paradox....Pages 97-105 Individual Gene Cluster Statistics in Noisy Maps....Pages 106-120 Power Boosts for Cluster Tests....Pages 121-130 Reversals of Fortune....Pages 131-141 Very Low Power to Detect Asymmetric Divergence of Duplicated Genes....Pages 142-152 A Framework for Orthology Assignment from Gene Rearrangement Data....Pages 153-166 Back Matter....Pages - This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative 'This volume contains the papers presented at the 3rd RECOMB Comparative Genomics meeting, which was held in Dublin, Ireland, on September 18-20, 2005.'