Database Commons

a catalog of biological databases

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

Database Profile

General information

URL: http://www.genomicus.biologie.ens.fr/genomicus
Full name: Genomes in Evolution
Description: Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes,transversaly across different species,and chronologicaly along evolutionary time.
Year founded: 2010
Last update: 2017-06-13
Version: v92.01
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: France
Data type:
Data object:
NA
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: IBENS
Address: Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, France
City: Paris
Province/State:
Country/Region: France
Contact name (PI/Team): Alexandra Louis
Contact email (PI/Helpdesk): alouis@biologie.ens.fr

Publications

25378326
Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics. [PMID: 25378326]
Louis A, Nguyen NT, Muffato M, Roest Crollius H.

The Genomicus web server (http://www.genomicus.biologie.ens.fr/genomicus) is a visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides access to genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants. Here we present the new features available for vertebrate genome with a focus on new graphical tools. The interface to enter the database has been improved, two pairwise genome comparison tools are now available (KaryoView and MatrixView) and the multiple genome comparison tools (PhyloView and AlignView) propose three new kinds of representation and a more intuitive menu. These new developments have been implemented for Genomicus portal dedicated to vertebrates. This allows the analysis of 68 extant animal genomes, as well as 58 ancestral reconstructed genomes. The Genomicus server also provides access to ancestral gene orders, to facilitate evolutionary and comparative genomics studies, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their putative gene targets. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 52 Citations (from Europe PMC, 2021-06-19)
23193262
Genomicus: five genome browsers for comparative genomics in eukaryota. [PMID: 23193262]
Louis A, Muffato M, Roest Crollius H.

Genomicus (http://www.dyogen.ens.fr/genomicus/) is a database and an online tool that allows easy comparative genomic visualization in >150 eukaryote genomes. It provides a way to explore spatial information related to gene organization within and between genomes and temporal relationships related to gene and genome evolution. For the specific vertebrate phylum, it also provides access to ancestral gene order reconstructions and conserved non-coding elements information. We extended the Genomicus database originally dedicated to vertebrate to four new clades, including plants, non-vertebrate metazoa, protists and fungi. This visualization tool allows evolutionary phylogenomics analysis and exploration. Here, we describe the graphical modules of Genomicus and show how it is capable of revealing differential gene loss and gain, segmental or genome duplications and study the evolution of a locus through homology relationships.

Nucleic Acids Res. 2013:41(Database issue) | 84 Citations (from Europe PMC, 2021-06-19)
20185404
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. [PMID: 20185404]
Muffato M, Louis A, Poisnel CE, Roest Crollius H.

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data. Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus.

Bioinformatics. 2010:26(8) | 123 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
384/5061 (92.432%)
Gene genome and annotation:
148/1350 (89.111%)
384
Total Rank
259
Citations
23.545
z-index

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Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2018-06-11]
Lina Ma [2016-04-13]
lin liu [2016-03-31]
lin liu [2016-03-29]
lin liu [2016-03-25]
Mengwei Li [2016-02-18]
Zhang Zhang [2015-12-31]
Jian Sang [2015-12-05]
Jian Sang [2015-06-28]
Li Yang [2015-06-26]