Development of a Web-based Genome Annotation System and Two Analysis Tools

Hongseok Tae1, Hyeweon Nam2, Daesang Lee, Kiejung Park, Dept. of Microbiology, Kyungpook National University;, Information Technology Institute, SmallSoft Co., Ltd.

We have developed a web-based genome annotation system. This system includes major modules such as gene prediction, homology search, promoter analysis, motif analysis, gene ontology analysis, annotation databases, and a genome browser which shows the entire information of a genome. The database saves the data obtained from each analysis module and the primary keys indicating the relationship between data. For the users' convenience, the database schemata are different for prokaryote and eukaryote genomes. Gene ontology analysis of prokaryotes is done using COGs and GO, and that of eukaryotes is done using GO. The genome browser module, which searches for the annotation results of an in-progress or finished genome project, visualizes the stored annotation data using the web-based graphical view. It also provides content search and the search results are shown as a list. More detailed information of each gene can be browsed by a further clicking. We have developed a motif analysis program and a gene prediction program, both of which are based on HMM. The gene prediction program, which has a general gene structure prediction model of eukaryotes, consists of a training set decomposition module, a training module, and a prediction module. The program is mainly focused on Rice Genome Analysis and more specific features will be added to improve the quality of Rice Genome Annotation.