Posted on décembre 26, 2009 by admin
ReNaBi’s platforms are providing many databases that represent key resources for the community.
These databases cover a wide range of topics:
Here is a listing of these databases.
Virus databases
Microbial sequence databases
| PlasmoDraft |
Database of Plasmodium falciparum gene function predictions based on postgenomic data |
| GenoList |
Integrated database for microbial genomes, with specialisation in population genomics of pathogens |
| CandidaDB |
Multi-genome database for Candida species and related Saccharomycotina |
| Molligen |
Database for comparative genomics of mycoplasma genomes; It contains about 20 bacterial (mycoplasma) (re)-annotated genomes |
| NORINE |
Unique database of nonribosomal peptides |
| CRISPRdb |
Database and tools to display CRISPRs and to generate dictionaries of spacers and repeats |
| GPMS Microbes Tandem Repeats Database |
Database of tandem repeats in microbes; On-line resources for bacterial micro-evolution studies |
| PkGDB |
Microbial genomes database for annotation and comparative analysis; >700 bacterial (re)-annotated genomes |
| ISFinder |
Insertion sequence database and service on IS expertise |
| COBALT |
Provides easy access to the results of multiple localization tools and support for predicting protein subcellular localizations for 784 whole bacterial and archaeal proteomes |
| MICADO |
Relational database dedicated to microbial genomes and functional analysis of B. subtilis |
| MOSAIC |
Relational database and web interface developed to compare closely related bacterial genomes |
| SPID |
Subtilis Protein interaction Database |
| Funybase |
Database dedicated to the analysis of fungal proteins extracted from complete public fungal genomes, and their classification in clusters of orthologs |
Plant & animal sequence databases
| OryGenesDB |
Database interoperability for functional genomics of rice |
| GreenPhylDB |
Database for structural, functional and comparative annotation dedicated to plant genomes and their bio-aggressors |
| PROTICdb |
Web-based application to store, track, query, and compare plant proteome data |
| Sigenae |
Sigenae contig browser: Aquaculture and farm animal species EST contigs access through Ensembl and BioMart |
| AphidBase |
An aphid genomics database and query tools |
| DGD |
Provides a list of groups of co-located and duplicated genes |
| ASSEMBLE Tools |
Tools and Databases dedicated to access of marine resources (ABiMS resource) |
| MICROBASE |
Microbotryum violaceum EST relational database |
| GnpIS |
Genetic & Genomic Information System with modular and interoperable databases and query interfaces allowing to query each database independently or in combination; it contains genetic (polymorphism, genotypes, phenotypes) and genomic data (sequences, mapping, expression…) from plant and fungi genomes (wheat, grapevine, maize, trees, fungi…) |
Human databases
| ITTACA |
A database of transcriptome arrays and clinical data of tumours |
| ACTuDb |
A database of array-CGH data of tumours |
| GENATLAS |
Contains relevant information with respect to gene mapping and genetic diseases; the information is collected from the literature |
| MIRIFIX |
Both an integrated database with its own developments and a dynamic portal to the most up-to-date and relevant webtools for non-coding RNA (miRNA); MIRIFIX(TM) enables questioning of microRNAs at each levels of action through a single interface |
Immunogenetics databases
| IMGT/LIGM-DB |
The IMGT® database for the nucleotide sequences of immunoglobulins (IG) and T cell receptors (TR) from human and other species of vertebrates, with translation of fully annotated sequences, created in 1989, on the Web since July 1995; 150,000 sequences from 254 species (human and other vertebrates) |
| IMGT/PRIMER-DB |
The IMGT® oligonucleotide database: Primers for combinatorial library constructions, single chain Fragment variable (scFv), phage display or microarray technlologies; 1,864 entries from 11 species (human and other vertebrates) |
| IMGT/GENE-DB |
The IMGT® gene database: Official repository of all the immunoglobulin (IG) and T cell receptor (TR) genes and alleles, approved by the WHO/International Union of Immunological Societies Nomenclature Subcommittee |
| IMGT/3Dstructure-DB |
The IMGT® 3D structure database: 3D structures of Immunoglobulins (IG), T cell receptors (TR), MHC, IgSF, MhcSF and related proteins of the immune system (RPI), created in November 2001; Repository of the amino acid sequences of the monoclonal antibodies and fusion proteins for immune applications (FPIA) of the WHO/International Nonproprietary Name (INN) programme |
| IMGT/mAb-DB |
The IMGT® database of therapeutic monoclonal antibodies and fusion proteins for immune applications (FPIA), created in 2009 |
| IMGT/CLL-DB |
IMGT/CLL-DB, the IMGT® database of IG sequences from patients with chronic lymphocytic leukemia, created in November 2007 |
Protein & motif databases
| MIPDB |
Database for intrinsic membrane proteins |
| PROSE |
Relational version of UniProt |
| HOVERGEN, HOGENOM & HOMOLENS |
Set of databases devoted to protein gene families |
| AT_Chloro |
Chloroplast proteome from Arabidopsis thaliana database |
| PRODOM |
Database of protein domains, part of the InterPro network |
Enzyme & pathway databases
| RBpathway |
Database of RB/E2F network |
| FUNGIpath |
Database and tool dedicated to metabolism pathway exploration in fungi; it currently contains 20 genomes data (Release 1.0, February 2009) |
| ORENZA |
Database of ORphan ENZyme Activities |
| Peroxibase |
Centralize most of the peroxidase superfamilies encoding sequences to follow the evolution of peroxidase among living organisms and to compile the information concerning putative functions and transcription regulation |
| MetExplore |
Database to link metabolomic experiments and genome-scale metabolic networks |
| PAREO |
Relational version of KEGG |
| UniPathway |
Curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase |
High-throughput data repositories
| GERMONLINE |
High-throughput expression data relevant for germline development across species (it includes data on the mitotic cell cycle in normal and malignant cells) |
| SIDR |
Standard-compliant metadata database with raw and/or processed associated data in Sytems biology |
Other databases
| GlycoBase |
Database of real NMR spectra concerning glycans from animal kingdom |
| ACNUC |
Sequence database management system for any collection in GenBank, EMBL or UniProt format |
