HCG: a database for hierarchical classification of functionally equivalent genes in prokaryotes

Background: The existing gene annotation schemes generally classify genes into two-levels of parallel and unrelated homologous and/or orthologous gene groups, limiting our capabilities for gene function prediction at higher resolution. While homology and orthology are useful concepts for evolutionary studies of genes, they may not be the most appropriate ones for functional classification of genes, especially at a high-resolution level. Results: We present a new gene annotation database: the hierarchical classification system of genes (HCG), which provides functional annotation of prokaryotic genes in general at higher resolution than the existing functional classification schemes. The HCG database consists of clusters, hierarchically organized, of functionally equivalent genes at varying levels of resolution. Gene clusters at the top of the HCG hierarchy representing homologous gene groups and descendent gene clusters representing functionally equivalent genes at an increasingly higher resolution going down from the top to the leaf-level clusters along the classification hierarchy. We also provide several examples t