BIOINFORMATICS<-->STRUCTURE
Jerusalem, Israel, November 17-21, 1996

Abstract

Working towards a comprehensive biological sequence comparison and analysis environment

David P. Yee(1)*, Frank Zucker(1), Tim Hunkapiller(1), Emir Pasalic(2), Justin Laird(2), Eric Hackborn(2)#, Johnny Helmich(2)#, Tom Stidham(2), Elizabeth Kutter(2) and Judith Bayard Cushing(2)

(1) Department of Molecular Biotechnology, University of Washington
(2)The Evergreen State College
* Current address: ZymoGenetics, 1201 Eastlake Ave East, Seattle, WA 98102
# Current address: Genomica

yee@zgi.com

The management and analysis of the enormous amount of biological data generated by large-scale DNA sequencing projects worldwide is a formidable problem. While it is of great interest to infer the biological function of novel genes as their sequences become available, predicting the function of genes that are only distantly related to known sequences can be extremely difficult. OverView is intended to represent and access biological sequences, the results obtained from the comparison of sequences against one another by multiple algorithms, and to infer properties of sequences by correlating the results obtained from multiple comparison methods. A conceptual data model for the representation of biological sequences and their properties is presented. The specification of a novel "cluster" tool that is generally useful for organizing and combining groups of sequences with similar properties is introduced. The current system is being developed in SmallTalk and is intended to be complementary to and interoperable with existing systems such as the object-oriented Genome Topographer developed by Tom Marr at Cold Spring Harbor.

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