Pasteur – Intégration et analyse Génomique
Posted on février 8, 2010 by adminCommentaires fermés sur Pasteur – Intégration et analyse Génomique
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Author Archive
PBIL – Lyon Gerland
Posted on février 8, 2010 by adminCommentaires fermés sur PBIL – Lyon Gerland
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IMGT (International Immunogenetic Information System)
Posted on février 8, 2010 by adminCommentaires fermés sur IMGT (International Immunogenetic Information System)
IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, 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 http://www.imgt.org (Montpellier, France) provides a common access to all Immunogenetics data.
web site : IMGT
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BioInfo-GenoToul
Posted on février 8, 2010 by adminCommentaires 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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MIG – INRA
Posted on février 8, 2010 by adminCommentaires 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:
- to develop methods and tools for analyzing genomic data in the following fields:
- Genome and evolution
- Automatic text analysis, data mining
- System biology
- 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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Databases
Posted on décembre 26, 2009 by adminCommentaires 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:
- Virus databases
- Microbial sequence databases
- Plant & animal sequence databases
- Human databases
- Immunogenetics databases
- Protein & motif databases
- Enzyme & pathway databases
- High-throughput data repositories
- Other databases
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 |
Proteomics
Posted on décembre 25, 2009 by adminCommentaires 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
RPBS
Posted on décembre 8, 2009 by adminCommentaires 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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