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Accurate evolutionary relationships for S4 were only uncovered with extensive coverage of the bacterial tree along with heavy use of genome content.
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The relative length of each chromosome segment was used as a measure of genome content so that the amount of coverage provided to each segment could be compared (Table 4).
Use of full genomes and subsequent gene-content profiling has thus become important for understanding the role of genome contents for defining a realized ecological niche [ 6].
Comparative primate genomics: emerging patterns of genome content and dynamics, Nature Reviews Genetics 15, 347 359 | doi 10.1038/nrg3707 (OA) Mike R. Perrin (2005).
In order to enable this type of genome content normalization, we used the same 31 Pfam profiles and the reciprocal search procedure to determine the number of genes belonging to our detoxification set in 835 fully sequenced and annotated bacterial genomes (Additional file 3).
We use a new method to evaluate the variation of genome content.
Here, we present two complementary bioinformatics strategies to perform more robust analyses of genome content and sequencing data, validated by use of the Saccharomyces cerevisiae fully sequenced genome.
Although genes are natural units in genome analysis there are some disadvantages to using genes as the central units in the analysis of the evolution of genome content.
The second property is the dynamics of genome content shuffling.
This tremendous new genomic information adds a new opportunity for systems biology, as it enables use of information about genome content for prediction of metabolic phenotypes of species in the gut [ 13], or to develop community systems [ 14] or supra-model organisms [ 15].
More detailed phylogenetic analysis of the genes used in the genome content analysis may be needed to test such an alternative.
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