Color graphics representations of large sequences in the GEM environment.

The analytical and descriptive color graphics capabilities (the GEM environment) of the CAGE/GEM(a) software system are described using bacteriophage lambda (48,502 base pairs) and Epstein Barr virus (172,282 base pairs) as examples. Genetics and features, as graphic drawings, and the results of sequence analysis as pseudo-colored representations, are simultaneously displayed at all zooming levels. The present upper limit on sequence size is 5 x 10(5) bases. The overlay editor utility which provides the capability to structure complex sequence associated data and knowledge bases into a manageable color graphics format is also described. Holistic correlations that can be made by the display of bacteriophage lambda and Epstein Barr virus in the GEM environment are also discussed.