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For microbial organisms, genome sequences are now commonly used as a basis for determining phylogenetic relationships.
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The case of study presented in this article evaluates all-against-all genomic comparisons between a set of microbial organisms, ie, each gene from a genome is compared to all genes from the other genomes.
There is an increasing availability of complete or draft genome sequences for microbial organisms.
Genomic signatures in terms of oligonucleotide distributions have widely been used for genome-based characterizations of microbial organisms (Bohlin et al., 2009).
As a consequence of DNA sequencing activities, whole-genome sequences for many microbial organisms as well as eukaryotic species are available in publicly accessible databases.
MEMOSys is an application for managing, developing, and storing genome-scale metabolic models of microbial organisms.
HOGENOM, for instance, is devoted to microbial organisms (bacteria, archaea and unicellular eukaryotes) with completely sequenced genomes, and does not intend to be exhaustive for multicellular organisms.
But of those we managed to recover the genomes for a little bit more than 1,500 microbial organisms.
In order to screen for the presence of any other microbial organisms in the experimental samples, the sequence reads were also mapped against viral, bacterial and archaeal genome databases.
Genome-scale metabolic network models have been successfully used to describe metabolic processes in various microbial organisms [ 12].
Many microbial organisms living in close association with other organisms in an obligate symbiotic or parasitic relationship also experienced a reduction in genome size with respect to their free-living ancestors.
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