MolliGen 3.0, evolution of a database dedicated to the comparative genomics of mollicutes

Aurélien Barré 1 Claire Lemaitre 2 Patricia Thebault 3, 4 Antoine de Daruvar 3, 4 Alain Blanchard 5 Pascal Sirand-Pugnet 5, *
* Corresponding author
1 CBiB-Centre de Bioinformatique de Bordeaux
CBIB - Centre de Bioinformatique de Bordeaux
2 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
5 UMR 1090
GD2P - Génomique, développement et pouvoir pathogène
Abstract : Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and of their pathogenicity for humans and for a broad range of animals and plants. An ever-growing number of genome sequences becomes available and constitutes a precious basis for a wide diversity of applied and fundamental researches including, development of typing markers, vaccine design, metabolic networks reconstructions, evolution and "omics" studies and, recently, synthetic biology. In order to provide tools for the comparative genomics of mollicutes to the scientific community, we have developed a web-accessible database named MolliGen. First released in 2004 with 6 genomes, MolliGen 3.0 now includes 26 genomes from 22 species. This new release of the database offers the possibility to compare public genomes with unpublished ones that can be loaded into private sections. As genome annotation update constitutes a constant necessity in genome databases, a re-annotation module was added that gives authorized users to modify gene annotation and to add or delete genetic elements. Search tools were improved to allow the formulation of complex queries in natural language. Results of queries can be saved as lists of CDSs over web sessions, combined with other lists and downloaded with chosen associated features. Homology relationships are available as pre-computed data or can be explored using blast queries, multiple alignments and motif search. Whole genome alignments and precise genome regions can be visualized using dedicated browsers. Many other tools were added or improved for the analysis and the comparison of genomes. The MolliGen 3.0 database is regularly updated and is available at http://cbib1.cbib.u-bordeaux2.fr/molligen/.
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https://hal.archives-ouvertes.fr/hal-00649151
Contributor : Patricia Thebault <>
Submitted on : Wednesday, December 7, 2011 - 10:57:36 AM
Last modification on : Friday, November 16, 2018 - 1:23:12 AM

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  • HAL Id : hal-00649151, version 1

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Aurélien Barré, Claire Lemaitre, Patricia Thebault, Antoine de Daruvar, Alain Blanchard, et al.. MolliGen 3.0, evolution of a database dedicated to the comparative genomics of mollicutes. Congress of the International Organization for Mycoplasmology ; 2010/07/11-16 ; Chianciano Terme (ITA). IOM congress 2010., 2010, Italy. ⟨hal-00649151⟩

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