Characteristics of biological data including genome sequences are heterogeneous and various. Although the need of management systems for genome sequencing which should reflect biological characteristics has been raised, most current biological databases provide restricted function as repositories for biological data. Therefore, this paper describes a management system of nucleotide sequences at the level of biological laboratories. It includes format transformation, editing, storing and retrieval for collected nucleotide sequences from public databases, and handles sequence produced by experiments. It uses BSML based on XML as a common format in order to extract data fields and transfer heterogeneous sequence formats. To manage sequences and their changes, version management system for originated DNA is required so as to detect transformed new sequencing appearance and trigger database update. Our experimental results show that applying active trigger rules to manage changes of sequences can automatically store changes of sequences into databases.