Author Archive

Pasteur – Intégration et analyse Génomique

Posted on février 8, 2010 by Commentaires fermés sur Pasteur – Intégration et analyse Génomique

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Posted on février 8, 2010 by Commentaires fermés sur PRABIG

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PBIL – Lyon Gerland

Posted on février 8, 2010 by Commentaires fermés sur PBIL – Lyon Gerland

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Posted on février 8, 2010 by Commentaires fermés sur PBIL Doua

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IMGT (International Immunogenetic Information System)

Posted on février 8, 2010 by Commentaires fermés sur IMGT (International Immunogenetic Information System)

IMGT®, the international ImMunoGeneTics information system®, is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species, created in 1989 by Marie-Paule Lefranc (Université Montpellier 2, CNRS). IMGT, a European project since 1992, works in close collaboration with EBI. IMGT consists of sequence databases (IMGT/LIGM-DB, a comprehensive database of IG and TR from human and other vertebrates, with translation for fully annotated sequences, IMGT/MHC-DB, IMGT/PRIMER-DB), genome database (IMGT/GENE-DB), structure database (IMGT/3Dstructure-DB), and monoclonal antibodies database, Web resources and interactive tools. The IMGT Home page (Montpellier, France) provides a common access to all Immunogenetics data.

web site : IMGT

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Posted on février 8, 2010 by Commentaires fermés sur BioInfo-GenoToul

The resources placed at the disposal of the scientific community are:

  • competences of a data processing and bioinformatic specialist  team
  • processing capacity of infrastucture of calculation
  • storage and provision capacity of data of the servers
  • accesses to the data banks generalist or specialized
  • software of the community bioinformatics

The missions of the bioinformatic platform are declined around 9 points:

  • To offer to the local community an adapted and powerful material and software infrastructure
  • To communicate on the evolution of the hardware, software, on the various actions undertaken on the platform
  • To train the users
  • To provide a support to the other local platforms
  • To provide a support bioinformatic to the priority scientific programs of biology and bioinformatic
  • To propose an animation around the bioinformatic platform
  • To place at the disposal of the working stations “framed” near the platform
  • To answer at the requests of expertise
  • To develop programs in dialogue with the local community and other Génopoles.

Link to the official site :


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Posted on février 8, 2010 by Commentaires fermés sur MIG – INRA

MIG is a laboratory with a strong interdisciplinary vocation that groups together mathematicians,
computer scientists, physical chemists and biologists for the analysis of genomic data.

MIG has two main tasks:

  1. to develop methods and tools for analyzing genomic data in the following fields:
    • Genome and evolution
    • Automatic text analysis, data mining
    • System biology
  2. to lend support to INRA biologists involved in genomic researches:
  • by collaborating with biologists about bioinformatics aspects of genomic projects, MIG is involved in about 20 ANR and European projects
  • by making available a bioinformatics platform that provides access to:
  • 15 servers, a cluster of 250 processors (3 Tflops/s), 50 Tb of disk, 46 biological databases, more than 100 bioinformatics softwares

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Posted on décembre 26, 2009 by Commentaires fermés sur Databases

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

GiantVirus Database on giant viruses
euHCVdb European Hepatitis C Virus database

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
Atlas of Genetics and Cytogenetics in Oncology and Haematology The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases.

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


Filed Under: Databases


Posted on décembre 25, 2009 by Commentaires fermés sur Proteomics

The ProteHome website, hosted by PRABI,  is a portal dedicated to resources for experimental proteomics by making these available to the scientific community. The aim of ProteHome is to contribute directly to the set up of services and resources for experimentalist and computer scientist involved in proteomics analysis and data handling.

MyProms An environment for mass spectrometry data management and analysis
PASE A web-based platform for peptide / protein microarray experiments.
ASCQ_ME Engine for peptide mass fingerprinting directly from mass spectrum

Filed Under: Proteomics


Posted on décembre 8, 2009 by Commentaires fermés sur RPBS


RPBS was initiated in the late 2003. His objectives are :

  • to provide a means of collaborative research in the field of structural bioinformatics at the level of Paris and beyond.
  • to provide some compendium of the services related to protein structure.

It is currently a joint effort of the following research groups from Paris.

  • MTi – Molécules thérapeutiques in silico – INSERM U973 – Université Paris 7
  • DSIMB – Dynamique des Structures et Interactions des Macromolécules Biologiques – INSERM U665 – Université Paris 7
  • ABI – Atelier de BioInformatique – Université Paris 6
  • IMPMC – Equipe Prédiction des Structures – CNRS UMR 7590 – Université Paris 6 et 7
  • IBBMC-MIP – Groupe Théorique de l’Equipe de Modélisation et Ingénierie des Protéines – CNRS UMR 8619 – Université Paris-sud 11
  • CNAM-STIC – Chaire de Bioinformatique, Conservatoire National des Arts et Metiers, Paris
  • MAP5 – Mathématiques Appliquées à Paris 5 – CNRS UMR 8145 – University Paris Descartes

Project coordination: P. Tufféry

Site web : RPBS

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