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Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms
Genes 2011, 2(4), 912-924; doi:10.3390/genes2040912

Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions

Received: 29 August 2011 / Revised: 7 October 2011 / Accepted: 25 October 2011 / Published: 9 November 2011
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
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The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show here for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, we do not find strong ubiquitous patterns governing the evolutionary behavior of specific functional classes. Instead, there are strong variations between the major groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints.
Keywords: protein domains; HMM models; GO classification; functional genome annotation; Eukarya protein domains; HMM models; GO classification; functional genome annotation; Eukarya
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Parikesit, A.A.; Stadler, P.F.; Prohaska, S.J. Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions. Genes 2011, 2, 912-924.

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