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After the bioinformatics software applies recognition algorithms that delineate individual genes (ORFs), then the ORFs are aligned with sequences of homologous genes of known function These two steps allow amino acid similarities in proteins encoded by new and previously characterized genes to be computed so that the biochemical function of the new genes can be tentatively assigned Several different levels of con dence for assigning gene function have been proposed (Kolker et al, 2005) and these vary, from high to low, depending upon the degree of similarity with known genes and proteins The template used by the US DOE Joint Genome Institute for categorizing and organizing genome sequence data is shown in Table 32 There are 23 functional categories of expected genes, known as COGs (clusters of orthologous groups) which span three well-established necessities of cellular life: information storage and processing , cellular processes , and metabolism .

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The remainder of genes in a genome fall into the poorly characterized category ( function unknown and general function prediction only ) Results of COG analysis for the 618 Mb genome (5452 ORFs) of Pseudomonas putida KT2440 are presented in Table 32 Note the high apportionment of this soil bacterium s genome to energy production (54%) and amino acid uptake and metabolism (95%); this issue will be revisited in Section 33 The poorly characterized or unknown hypothetical category of genes is a barometer for the completeness of our understanding of prokaryotic genomes and (by inference) prokaryotic biology The proportion of unknown hypothetical genes in all genome-sequencing projects hovers at roughly one-third (eg, Kolker et al, 2005) This proportion of unknown hypothetical genes even applies to the thoroughly studied bacterium, E coli.

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While it is possible that poorly characterized genes have no function (they may be noncoding or junk DNA), it is equally plausible that these genes are blatant reminders of how little we truly understand about real-world ecological pressures and the physiological processes expressed by microorganisms in their native habitats Because laboratory cultivation of microorganisms likely fails to mimic the physiological and ecological conditions experienced by microorganisms in eld settings, many genetic traits may go unexpressed by the organism; hence, unobserved by the microbiologist Understanding the function of unknown hypothetical genes represents one of the major frontiers in biology The lack of knowledge of a signi cant proportion of each microbial genome limits our ability to advance biology to a more predictive science (Kolker et al, 2005) Thus, although genomics has provided genetic blueprints for individual microorganisms, a substantial proportion of the blueprints remains illegible and mysterious..

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Realizing the scienti c wealth of these experiments presents new problems in data access, processing and distribution, and collaboration across national and international networks, on a scale unprecedented in the history of science. The information technology challenges include the following:

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