Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://ioda.univ-provence.fr
Full name:
Description: The chordate proteome history database comprises some 20,000 evolutionary analyses of proteins from chordate species. The main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches.
Year founded: 2012
Last update:
Version:
Accessibility:
Manual:
Unaccessible
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Country/Region: France
Data type:
Data object:
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: Aix Marseille University
Address: INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix Marseille Université, ESIL Polytech, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
City:
Province/State:
Country/Region: France
Contact name (PI/Team): Anthony Levasseur
Contact email (PI/Helpdesk): anthony.levasseur@univ-amu.fr

Publications

22904610
The chordate proteome history database. [PMID: 22904610]
Levasseur A, Paganini J, Dainat J, Thompson JD, Poch O, Pontarotti P, Gouret P.

The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.

Evol Bioinform Online. 2012:8() | 1 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
4993/5061 (1.363%)
Phylogeny and homology:
213/216 (1.852%)
4993
Total Rank
1
Citations
0.111
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Record metadata

Created on: 2018-01-29
Curated by:
Pei Wang [2018-03-08]
Pei Wang [2018-02-25]