Sophisticated information strategies are increasingly essential for biologists. We have built a powerful knowledge discovery resource using novel genomic context methods, interactive visualization strategies, and computational environment technologies. The Heuristic Entity Relationship Building Environment (HERBE) is a research platform for advanced database technologies that fuses data management solutions with knowledge management components to support the dynamic capture of concepts and observations as biologists explore large-scale data. The Similarity Box visualization software supports the ability of biologists to interact with large-scale computational results and evaluate relationships based on natural reasoning processes. We have applied these knowledge methods in the exploration of complex microbial genome relationships. We extracted a complete set of gene neighbor patterns for Rhodobacter sphaeroides using HERBE to map data structures for chromosomal contiguity against sequence similarity. We then organized these gene neighbor patterns by their phylogenetic profiles using Similarity Box to enable biologists to explore the results.