An interactive graphic viewer, ChromoScope, was developed to explore scientific visualization of complicated genome data. Escherichia coli was selected as the test organism. An ASN.1 data set has been built for the entire E. coli chromosome, including a genetic map, a physical (ordered restriction) map, the alignment between the two maps, Kohara clones and some short repeat features. The E. coli sequence is modeled as a segmented sequence, incorporating both the sequence and the physical map data. The alignment between the contig and the published sequences is stored as sequence history, allowing direct access to the same sequence in the public databases. The alignment is displayed graphically, with both the sequence alignment and feature annotations. The alignment viewer also supports a detailed text display, providing information to resolution at residue level with annotated features.