Microbial genome annotation system and VNTR search algorithm

Abstract

A Web based microbial Genome Annotation System (WeGAS) was developed that provides several features required in genome annotation, such as gene prediction, homology search, promoter/motif analysis, genome browsing, gene ontology analysis based on the COGs and GO, and metabolic pathway analysis, with web-based interfaces. Most raw data and intermediate data from genome projects can be managed by the WeGAS database system, and analysis results, including information on each gene and final genome maps, are provided by its visualization modules. Especially, a pie-view browser displaying circular maps of contigs and a COG-GO combination browser are very helpful for an overview of projects. Major public microbial genome databases can be imported, searched, and browsed through the WeGAS modules. WeGAS is freely accessible for academic users via web site http://ns.smallsoft.co.kr:8051. A tandem repeat is defined as a sequence of two or more contiguous, similar copies of a pattern of nucleotides. Tandem repeat sequences have many applications fields including typing microbes, disease diagnosis, mapping studies, DNA fingerprinting in forensic field, sequences homology, and population studies. In this thesis, new algorithm for finding variable number of tandem repeats (VNTR) was developed. This algorithm consisted of three stages. One is to find seed-unit pair which has max alignment score, another is to extend seed-unit to candidate unit which has max score and the third is to enlarge candidate unit to find tandem repeat region score. The global alignment method was used in the each stage to find tandem repeat region. The data of predicted VNTR regions were integrated into the local genome database and could be viewed by VNTR viewer in the WeGAS.