Genomic sequences provide catalogs of genomic features that ultimately interact with the environment to determine our biology, physiology, and disease susceptibility. Comparing genomic properties of different organisms is of fundamental importance in the study of biological and evolutionary principles. Completion of hundreds of genome sequences gives us possibility for the genome-wide comparisons and for identification of genes or genomic regions underlying the many features that distinguish taxonomic groups and species. DNA and amino acid sequences contain information about both the phylogenetic relationships among species and the evolutionary processes that caused the sequences to divergence. Comparative genomics offers large-scale analysis of genomes from multiple species and gives us new insights into genome evolution and the way natural selection moulds DNA sequence. The computational challenges in this area are many and often very hard since questions about genomes are much more complex than analogous questions about DNA or protein sequences.

This special issue will be mainly focused on computational, evolutionary, and functional aspects of analyzing and comparing genomes. We invite authors to present original research articles as well as reviews that will stimulate continuing effort toward reconstructing the process that shaped genomes on the way from bacteria to humans. The special issue will become international forum for researchers to summarize the most recent developments in the field. The topics to be covered include, but are not limited to:

• Construction of syntenic blocks from genome data
• Gene family evolution
• Gene structure evolution
• Transposable elements
• Horizontal transfer
• Genome duplication
• Models and algorithms for genome rearrangements
• Reconstruction of ancestral genomes
• Phylogenetic reconstruction from whole genomes

Before submission authors should carefully read over the journal's Author Guidelines, which are located at http://www.hindawi.com/journals/abi/guidelines/. Prospective authors should submit an electronic copy of their complete manuscript through the journal Manuscript Tracking System at http://mts.hindawi.com/ according to the following timetable: