A database system for constructing, integrating, and displaying physical maps of chromosome 19

Eflords are underway at numerous sites around the world lo construct physical maps of all human chromosomes. These maps will enable researchers to locate, characterize, and eventually understand the genes lhat control human structure and function. The volume and complexity of Ihe data already generated requires a sophislicated array of compu2ational support to collect, store, analyze, integrate, and display in biologically meaningful ways. The Human Genome Center at Livermore has spent the past 6 years constructing a database system to support its physical mapping efforts on human chromosome 19. Our computa2ional support team is composed of experienced computer professionals who share a common pragmatic primary goal of rapidly supplying tools that meet Ihe ever-changing needs of the biologisls. In this paper we concentrate on -the design issues, tradeoffs, and consequences from the point of view of building a complex database system to support leading-edge genomic research. We introduce Ihe topic of physical mapping, discuss Ihe key design issues involved in our database, and discuss the use of this data by our major tools (DNA fingerprint analysis and overlap computation, condig assembly, map inlegration, and database browsing.) Given the advantage of hindsight, we discuss what worked, what didn’t, and how we will evolve from here. As early pioneers in this field we hope that our experience may prove useful to oth,ers who are now beginning to deszgn and construcl similar systems.