Paul Bieganski

Implementation and testing of an automated EST processing and similarity analysis system

Expressed sequence tag (EST) sequencing projects are being undertaken in an effort to identify the function of as many genes as possible from entire genomes. Putative function can be determined by analyzing the similarity of the ESTs to sequences in the public databases. We are involved in a long-term project to research and develop database technology to store and analyze ESTs for Arabidopsis thaliana. The massive amounts of ESTs being produced through automated sequencing technologies necessitates the automated processing and similarity analysis of the ESTs. This paper describes a complete software system that takes ESTs from a sequencing machine, analyzes them for quality, and searches in public databases of previously known sequences. Automating the processing and analysis of the several thousand ESTs produced to date by the Michigan State University, Arabidopsis cDNA Sequencing Project has improved the quality of the EST data and the speed at which ESTs can be entered in the public databases.<<ETX>>

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 afkt 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 ermy of amotated sequence fragments as they are produced by sequencing machines, storing the fragmenta in the database, and automatically prcducing and displaying similarity search results of new sequences against the large public sequence datsbsses GenBank and PIR. This paper describes the prototype, discusses the kme!its of object-oriented databases for complex and changing sequence da@ 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 tieebased data stnscture that supports rapid similarity searches on sequence data is introduced. Finally, future plans for the system are discussed.