PhylomeDB: a database for genome-wide collections of gene phylogenies - PubMed (original) (raw)

. 2008 Jan;36(Database issue):D491-6.

doi: 10.1093/nar/gkm899. Epub 2007 Oct 25.

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PhylomeDB: a database for genome-wide collections of gene phylogenies

Jaime Huerta-Cepas et al. Nucleic Acids Res. 2008 Jan.

Abstract

The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.es.

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Figures

Figure 1.

Figure 1.

Screenshot of a PhylomeDB entry page. The entry page of an individual seed protein (Hsa0017176) of the human phylome (Hsapiens001), includes information on the sequence and links to (i) the feature page containing all necessary information of the phylogenetic pipeline used; (ii) all the phylogenetic trees derived by the different programs and models used in the pipeline, in this case a NJ tree, ML trees derived from JTT, WAG, RtREV and BLOSUM62 models, and the consensus tree derived from the Bayesian analyses; (iii) the raw and trimmed (clean) alignments and (iv) the list of tree-based orthology predictions for the species included in the tree.

Figure 3.

Figure 3.

Visualization of phylogenetic trees: different views of the ML phylogenetic tree, using JTT evolutionary model, for the seed protein (Hsa0017176), as displayed by the environment for tree exploration tool (ETE). Trees can be represented in rectangular (A), circular (B) or radial (C) modes. Several information labels such as support values or branch distances (A) can be displayed on nodes and edges, which can also be colored to indicate different evolutionary event. In (A) an example is shown where the lineages leading to the seed protein (Hsa0017176) are colored in blue or red to mark duplications and speciation events, respectively. This feature is shown after running the orthology prediction algorithm by clicking on the ‘orthologs’ icon. Using the ETE toolbar (icons on the top of the section A), the user can navigate within the tree and browse it using different visualization options.

Figure 2.

Figure 2.

Visualization of multiple sequence alignments: Example of the trimmed (clean) multiple sequence alignment of the example entry (Hsa0017176) as displayed by JalView (17). Sequence names are indicated by PhylomeID names, which include the three-letters species code followed by a number. The levels of sequence conservation and quality of each column, as well as a consensus sequence are indicated bellow. Colors, sequence format and visualization options can be changed using JalView interface.

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References

    1. Sicheritz-Ponten T, Andersson SG. A phylogenomic approach to microbial evolution. Nucleic Acids Res. 2001;29:545–552. - PMC - PubMed
    1. Gabaldón T. Evolution of proteins and proteomes, a phylogenetics approach. Evol. Bioinform. Online. 2005;1:51–56. - PMC - PubMed
    1. Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon T. The human phylome. Genome Biol. 2007;8:R109. - PMC - PubMed
    1. Comas I, Moya A, Gonzalez-Candelas F. From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case. Syst. Biol. 2007;56:1–16. - PubMed
    1. Gabaldón T, Huynen MA. Reconstruction of the proto-mitochondrial metabolism. Science. 2003;301:609. - PubMed

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