Comparative Genomics

This book constitutes the refereed proceedings of the 4th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2006. The 17 revised full papers presented were carefully reviewed and selected from 34 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.

Reconstructing Domain Compositions of Ancestral Multi-domain Proteins. - Domain Architecture in Homolog Identification. - Inferring Positional Homologs with Common Intervals of Sequences. - On Genome Evolution with Accumulated Change and Innovation. - Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes. - Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution. - How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation. - Sorting by Translocations Via Reversals Theory. - Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. - Ordering Partially Assembled Genomes Using Gene Arrangements. - Evolution of Tandemly Repeated Sequences Through Duplication and Inversion. - A PQ Framework for Reconstructions of Common Ancestors and Phylogeny. - Intron Loss Dynamics in Mammals. - Finding Maximum Likelihood Indel Scenarios. - Conservation Patterns in cis-Elements Reveal Compensatory Mutations. - Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps. - Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer.