The gap between the increasing amount of raw sequence data and qualified biological information is widening: it is not possible to provide qualified annotation for new genomes with the same speed at which sequences are generated -- especially with next generation sequencing technologies. Additionally, managing the huge number ofavailable bioinformatics algorithms represents a challenge of its own. Thus, a systemwhich provides maximum annotation quality with approved methods in a minimum of time is absolutely critical as the basis for the R&D pipeline in industrial biotechnology. Also using those various genome annotation, comprehensive knowledge of a fungal’s biosynthetic capacities is the indispensable basis of its usefulness in the biotechnology research. Comparative genomics is on the rise as a potent tool in molecular biology. The publicly available genomes from yeasts and several fungal species are used to comparative genomics method for discovery of functional information in our research. Also we had integrated information from different data sources to dynamically build semantic networks representing up-to-date knowledge, which can then be mined and analyzed. Through those methods, we could inspect the common features and uniques between yeasts and fungal species in the new aspect.