AUGUSTUS [4] is a DNA-sequence-based gene prediction program for eukaryotes, i.e. organisms with a cell nucleus. The purpose of the program is to identify the location and structure of all protein-coding genes in a given genome. Gene prediction is the first and most important step in the analysis of newly sequenced organisms. During the last years, AUGUSTUS has been used in many genome projects, e.g. [6] and [7]. A web interface for AUGUSTUS has been available at the website of the Bioinformatics group in Göttingen for several years [8]. Because the computing power of the group is limited, the web interface only allows the input of relatively short sequences, up to 3 million base pairs.