Bases de données


IGM

Bacterial Genotyping

Base de données de génotypage pour différents microorganismes.
Microbes genotyping databases.
I Grissa, P Bouchon, C Pourcel and G Vergnaud. On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing. Biochimie Volume 90, Issue 4, April 2008;660-668.
IGM

BAGET

Service Web pour la recherche sans effort des gènes procaryotes et de leur séquence.
Web server for the effortless retrieval of prokaryotic gene context and sequence.
J. Oberto. BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence. Bioinformatics 2008 24(3):424-425.
IGM

CorBank

Base de données permettant la correspondance entre les identifiants protéiques de RefSeq, Genome Reviews et UniProt ainsi que la détection d'éventuelles différences entre bases de données des génomes de référence.
Database for immediate matching protein identifiers of RefSeq, Genome Reviews and UniProt and for detecting any differences between curated genome databases.
Descorps-Declère S, Barba M, Labedan B. Matching curated genome databases: a non trivial task. BMC Genomics. 2008 Oct 24;9:501.
IGM

CRISPR

Base de données regroupant les CRISPRs (Clustered Regulary Interspacing Short Palindromic Repeats) identifiés dans les génomes publiés.
Database of CRISPRs (Clustered Regulary Interspacing Short Palindromic Repeats) identified in published genomes.
I. Grissa, G. Vergnaud and C. Pourcel. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007 May 23;8(1):172.
IGM

FUNGIpath

Base de données permettant de comparer le métabolisme primaire et secondaire de différentes espèces fongiques.
Database to compare the primary and secondary metabolism of different fungal species.
Grossetete S, Labedan B, Lespinet O. FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. BMC Genomics. 2010 Feb 1;11(1):81.
KEGG licence ftp

KEGG

Kyoto Encyclopedia of Genes and Genomes
licence de connection ftp pour l'Université Paris-Sud : ftp://ftp.bioinformatics.jp/

Kyoto Encyclopedia of Genes and Genomes
IGM

NAPP database

Nucleic Acids Phylogenetic Profiling
Prediction of functional non-coding RNA in Bacteria and Archaea.
Ott A, Idali A, Marchais A & Gautheret D. (2012) NAPP: the nucleic acid phylogenetic profile database. Nucl. Acids Res. 40 (D1): D205-D209.
IGM

ORENZA

Base de données des Activités Enzymatiques Orphelines.
Database of ORphan ENZyme Activities.
Lespinet O and Labedan B ORENZA: a web resource for studying ORphan ENZyme Activities. BMC Bioinformatics. 2006 Oct 6;7:436.
IGM

Podospora

Base de données regroupant les données de séquençage et d'assemblage du génome de Podospora anserina.
Database of data assembly and sequencing the genome of Podospora anserina.
Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Ségurens B, Poulain J, Anthouard V, Grossetete S, Khalili H, Coppin E, Déquard-Chablat M, Picard M, Contamine V, Arnaise S, Bourdais A, Berteaux-Lecellier V, Gautheret D, de Vries RP, Battaglia E, Coutinho PM, Danchin EG, Henrissat B, Khoury RE, Sainsard-Chanet A, Boivin A, Pinan-Lucarré B, Sellem CH, Debuchy R, Wincker P, Weissenbach J, Silar P The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol 2008, 9:R77
IGM

The ppRNome Browser


(or here in case the main link is unavailable)
Genome Browser to display experimental data of a whole-genome mapping of 5' RNA ends in Enterococcus faecalis Innocenti N, Golumbeanu M, Fouquier D'HérouëL A, Lacoux C, Bonnin RA, Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis. RNA. 2015, 21(5):1018-30
INRA Le Moulon

PROTICdb

Base de données protéomique: gels 2D et spectrométrie de masse.
Proteomics database: 2D gels and mass spectrometry.
Ferry-Dumazet H, Houel G, Montalent P, Moreau L, Langella O, Negroni L, Vincent D, Lalanne C, de Daruvar A, Plomion C, Zivy M, Joets J. PROTICdb: a web-based application to store, track, query, and compare plant proteome data. Proteomics. (2005) May;5(8):2069-81
Langella O, Zivy M, Joets J.The PROTICdb database for 2-DE proteomics.
Langella O, Valot B, Jacob D, Balliau T, Flores R, Hoogland C, Joets J, Zivy M.Management and dissemination of MS proteomic data with PROTICdb: example of a quantitative comparison between methods of protein extraction.Methods Mol Biol. 2007;355:279-303
IGM/LRI

SynteView

Base de données regroupant les données de synténie de 600 génomes complement séquencés et comparés entre eux.
Database of data synteny of 600 completely sequenced genomes and compared them.
Lemoine, F.; Labedan, B. & Lespinet, O. SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. BMC Bioinformatics, 2008, 9, 536.
IGM

Tandem Repeats

Base de données présentant les répétitions en tandem de génomes, notamment bactériens, publiés.
Database of tandem repeats from publicly available microbial genomes.
F. Denœud and G. Vergnaud. Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource. BMC Bioinformatics 2004, 5:4
P. Le Flèche, Y. Hauck, L. Onteniente, A. Prieur, F Denoeud, V. Ramisse, P. Sylvestre, G. Benson, F. Ramisse and G. Vergnaud. A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiology 2001, 1:2