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The gastric pathogen H. pylori have multiple complete genomes available on public databases for scientific exploitation.
Rather than working with a single reference, Ragout uses multiple complete genomes from closely related species/strains.
This situation started to change when comparison of multiple, complete genomes of prokaryotes (archaea and bacteria) became possible towards the end of the last century.
Sequences of multiple, complete genomes of eukaryotes from various lineages enabled reconstruction of ancestral gene structures and of evolutionary trajectories that led to the modern genes [ 38].
The analysis presented here is based on multiple complete genomes belonging to organisms from the three cellular domains, along with current biochemical knowledge.
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The availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof.
The availability of multiple complete genome sequences from the whole spectrum of life, along with corresponding protein sequence data sets and more sophisticated bioinformatics tools opens a window into the intricate mechanisms of cellular evolution.
The determination of multiple, complete genome sequences of bacteria, archaea and eukaryotes has created the opportunity for a new level of phylogenetic analysis that is based not on a phylogenetic tree for selected molecules, for example, rRNAs, as in traditional molecular phylogenetic studies [ 1, 2], but (ideally) on the entire body of information contained in the genomes.
To place this finding into context, Listeria species have been reported as having the strongest purifying selection (elevated synonymous mutation rates) of all the prokaryotes following comparison of multiple completed genome sequences [ 37].
As long as multiple complete, finished genomes of the organism of interest are available, it will be possible to define a core genome and to apply it to derive accessory genomic sequence from query genomes using these tools.
Multiple complete apicomplexan genomes (Heiges et al., 2006; Gajria et al., 2008; Aurrecoechea et al., 2009) were also searched for LDH and MDH homologs in order to fill out the apicomplexan portion of the tree (using a more lenient significance cutoff of E-values <10−4).
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