New metrics for comparative genomics

Abstract

The availability of genome sequences from a variety of organisms presents an opportunity to apply this sequence information to solving the key problems of molecular biology. One of the principal roadblocks on this path is the lack of appropriate descriptors and metrics that could succinctly represent the new knowledge stemming from the genomic data. Several new metrics have recently been used in comparative genome analysis, yet challenges remain in finding an appropriate language for the emerging discipline of systems biology.

Figure 1

The tree of life in three dimensions. The plot, taken from [8^•], reflects the ‘genome conservation’ and ‘horizontal gene transfer vine width’ data. Individual taxonomic nodes are shown as white spheres, the diameters of which reflect the number of node-specific gene families. The bacterial phylogenetic tree is in cyan and the archaeal tree in light green. Red lines indicate the horizontal gene transfer. The width of each line reflects the number of gene families transferred along that line. Reprinted with permission from Genome Res 2005, 15:954–959.

Figure 2

Functional category profiles of four bacterial genomes. The plot shows the number of proteins from Dechloromonas aromatica RCB (front row; cream), Rhodopseudomonas palustris HaA2 (second row; magenta), Shigella dysenteriae Sd197 (third row; blue) and Mycobacterium avium subspecies paratuberculosis K-10 (back row; cyan), assigned to COGs in each functional category. COG functional categories are grouped as follows: 1, information storage and processing (J, translation, ribosomal structure and biogenesis; K, transcription; L, DNA replication, recombination and repair); 2, metabolism (C, energy conversion; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid metabolism; P, inorganic ion transport and metabolism; Q, secondary metabolism; V, defense mechanisms); 3, cellular processes (D, cell division; M, cell envelope; N, motility and secretion; O, post-translational modification and protein turnover; T, signal transduction; U, intracellular trafficking); and 4, poorly characterized (R, general function prediction only; S, unknown function). The data are taken from the Entrez Genome database (http://www.ncbi.nlm.nih.gov/sutils/coxik.cgi?gi=18621 and similar entries).