Recently, construction of physical maps based on YAC and cosmid contigs has become increasingly common, since these maps serve as a fine-scale ordering basis for gene searches. We describe a combination of visualization and database tools that address this problem. The YAC-Cosmid contig tool is a map visualization and editing tool designed for large data sets. The Physical Map Assembler (PMA) uses a rule-based interval-ordering approach to infer ordering from experimental data. It is implemented as an active object-oriented database. The PMA visualizer displays interval orderings in a comprehensible fashion, and thus helps the scientist resolve conflicts and ambiguities identified by PMA. Both visualization tools let the user query the database to see the details behind the picture. We have found that a tight integration of visualization and analysis tools with the database enhances their usability, and speeds up the dual tasks of analyzing and understanding the experimental data. The use of our tools is illustrated by examples from a gene search at the University of Michigan Genome Center.