The RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG) is a forum on all aspects and components of Comparative Genomics ranging from new quantitative discoveries about genome structures and processes to theorems on the complexity of computational problems inspired by genome comparison. Due to the interdiciplinary nature of the workshop, papers could be submitted merely for presentation at the workshop or for presentation at the workshop and publication in the proceedings. Speakers presenting papers of the former category are listed under Selected Presentations below. The workshop was a great success scienti?cally as well as socially. I want to thank all participants, the members of the program committee as well as referees and, especially, the excellent invited speakers. October 2004 Jens Lagergren Invited Speakers Mathieu Blanchette (McGill University, Canada) Daniela Delneri (University of Manchester, UK) Henrik Kaessmann (Universit e de Lausanne, Switzerland) Martin Lercher (University of Bath, UK) Bill Martin (Heinrich-Heine Universit at, Germany) Ben Raphael (UCSD, USA) Marie-France Sagot (Universit e Lyon I, France) Graziano Pesole (University of Milan, Italy) Selected Presentations Ali Bashir (UCSD, USA) Inna Dubchak (Lawrence Livermore National Laboratory, USA) Dannie Durand (Carnegie Mellon University, USA) Ron Y.

Includes supplementary material: sn.pub/extras

Inhalt
Conservation of Combinatorial Structures in Evolution Scenarios.- Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search.- Multiple Genome Alignment by Clustering Pairwise Matches.- On the Structure of Reconciliations.- The Statistical Significance of Max-Gap Clusters.- Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes.- Genome Rearrangement in Mitochondria and Its Computational Biology.- The Distribution of Inversion Lengths in Bacteria.- Estimators of Translocations and Inversions in Comparative Maps.- Databases for Comparative Analysis of Human-Mouse Orthologous Alternative Splicing.