We previously developed a relational schema for effectively building, integrating, and searching the DNA database on the relational database management system, SYBASE, at DDBJ. The schema is named the "DDBJ schema". The schema allowed us to implement a DNA database management system with two types of window interfaces, YAMATO and ASUKA, to easily build the DNA database. The first type with the DDBJ-schema is utilized by reviewers (DDBJ support staffs) for processing a single entry sent by an author. The second type with it is utilized by the Human Genome Project for processing multiple entries. Both also have a window interface similar to the flat file format. Finally, we developed two additional systems for both YAMATO and ASUKA. One is a restructuring tool to convert data with the GenBank-schema into those with the DDBJ-schema when we move AWB to the new system. The other is a tree search tool needed to repair the existing taxonomy database which is including many kinds of errors. A structured SQL-programming method is proposed to be used to implement these additional systems. The method is developed through the SQL expression and the control flow language (CFL) of SYBASE, and allowed us to implement the restructuring tool and the tree search tool.