Genome and metagenome sequencing is increasingly turned to as means to understand the functional diversity and adaptive mechanisms of microorganisms. Worldwide sequencing efforts have produced a deluge of data, which must now be transferred into biological knowledge. Several annotation systems have been developed to facilitate this process, such as GenDB, developed at University of Bielefeld. JCoast is a Java-based software tool, which effectively runs as an extension of existing GenDB v2.2 annotation projects. The major improvement rises from JCoast's ability to facilitate rapid and comprehensive comparison of a reference genome with respect to additional genomes, and even metagenomes. It was designed to allow biologists a rapid overview of genome and metagenome projects, using sortable tables to display the information. The JCoast workbench provides search tools and statistical methods to efficiently and intuitively answer questions of comparative genomics. View the screenshot gallery to get some impressions.