An object-oriented genetics information system

Sequence data is being produced by genomic sequencing laboratories at ever-increasing rates, making it impossible for individual researchers to keep track of all the new data that might affect their research. Computer systems are needed so that researchers can access this data. The systems must support high-level interfaces that communicate in the language of the researchers, database systems that guarantee availability and consistency of the data, and powerful search systems that rapidly scan for similarities between sequences. We have developed a prototype system that includes a graphical user interface, an object-oriented database management system, and high-performance similarity search algorithms. The prototype has the potential to increase researchers' productivity by automating entry of annotated sequence fragments as they are produced by sequencing machines, storing the fragments in the database, and automatically producing and displaying similarity search results of new sequences against the large public sequence databases GenBank and PIR. This paper describes the prototype, discusses the benefits of object-oriented databases for complex and changing sequence data, and presents an object-oriented schema for genetic information. Graphical tools for annotating sequences, storing them in the database, automating similarity searches, and viewing similarity search results are presented. A new suffix treebased data structure that supports rapid similarity searches on sequence data is introduced. Finally, future plans for the system are discussed.