Posts Tagged Databases

Databases

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

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Filed Under: Databases

GenOuest

Posted on décembre 6, 2009 by Commentaires fermés sur GenOuest

Logo_BioInfoGenouest

GenOuest is a bioinformatics platform hosted by INRIA Rennes Bretagne-Atlantique center and IRISA. This platform acted primarily as a core facility and software tool provider for the analysis of genomic data generated by the different laboratories of Biogenouest (formerly OUEST-genopole®). The plate-forme is IBiSA labelled since 2009.

The platform provides a complete bioinformatics environment: computing power, storage, databanks and also a comprehensive list of software dedicated to sequence analysis. On a national level, the platform is developing an expertise in the field of pattern matching and pattern discovery tool. This activity results from a tight interaction between the GenOuest platform and the Symbiose research team (INRIA).

Among its activities GenOuest is involved in many development projects: user-oriented tools or technological transfer of new algorithms elaborated by Symbiose.
The platform is a member of the GRISBI platform, a joined project between six French bioinformatics platform aiming at the deployment of a bioinformatics grid. GenOuest is also a member of the MobyleNet project.

GenOuest is also providing a complete cursus of bioinformatics training: tools, methodologies, programming languages.

The platform is ISO9001:2000 certified since may 2008.

Outline :

People :

8 persons (2 on a permanent position)

Computer resources

2 clusters (200 cores) / 50 Tb storage

Hosted databases and specific public resources

  • Germonline
  • Mimas
  • Aphidbase
  • Autograph
  • Phymycodb
  • Rasta bacteria

Specific software

  • Stan
  • Wapam
  • Pygram
  • Logol
  • Protomata
  • Plast
  • iThos

Projects

  • GRISBI
  • MobyleNet
  • BioWIC

Training

The whole list of courses is available  here



Web site  : GenOuest

Logo_BioInfoGenouest

GenOuest is a bioinformatics platform hosted by INRIA Rennes Bretagne-Atlantique center and IRISA. This platform acted primarily as a core facility and software tool provider for the analysis of genomic data generated by the different laboratories of Biogenouest (formerly OUEST-genopole®). The plate-forme is IBiSA labelled since 2009.

The platform provides a complete bioinformatics environment: computing power, storage, databanks and also a comprehensive list of software dedicated to sequence analysis. On a national level, the platform is developing an expertise in the field of pattern matching and pattern discovery tool. This activity results from a tight interaction between the GenOuest platform and the Symbiose research team (INRIA).

Among its activities GenOuest is involved in many development projects: user-oriented tools or technological transfer of new algorithms elaborated by Symbiose.
The platform is a member of the GRISBI platform, a joined project between six French bioinformatics platform aiming at the deployment of a bioinformatics grid. GenOuest is also a member of the MobyleNet project.

GenOuest is also providing a complete cursus of bioinformatics training: tools, methodologies, programming languages.

The platform is ISO9001:2000 certified since may 2008.

Outline :

People :

8 persons (2 on a permanent position)

Computer resources

2 clusters (200 cores) / 50 Tb storage

Hosted databases and specific public resources

  • Germonline
  • Mimas
  • Aphidbase
  • Autograph
  • Phymycodb
  • Rasta bacteria

Specific software

  • Stan
  • Wapam
  • Pygram
  • Logol
  • Protomata
  • Plast
  • iThos

Projects

  • GRISBI
  • MobyleNet
  • BioWIC

Training

The whole list of courses is available  here



Web site  : GenOuest

CBIB Bordeaux

Posted on décembre 6, 2009 by Commentaires fermés sur CBIB Bordeaux

Le Centre de Bioinformatique de Bordeaux (CBIB) a pour vocation de fédérer et de stimuler les projets de recherche en bioinformatique, de satisfaire les besoins bioinformatiques liés aux activités de recherche des laboratoires de biologie de la région et d’être un centre de ressources ouvert à l’ensemble de la communauté par la mise à disposition de services en accès public via le WEB.

La recherche en bioinformatique du CBiB se développe autour de deux axes :

  • l’application à la biologie de travaux de recherche en informatique menés au Laboratoire Bordelais de Recherche en Informatique (LaBRI) de l’Université Bordeaux 1,
  • le développement de nouvelles méthodes et de nouveaux outils pour exploiter les données de génomique et de génomique fonctionnelle.

Pour satisfaire les besoins des laboratoire de biologie, le CBIB :

  • assure la mise à disposition et la maintenance de ressources publiques (bases de données, programmes…) sur son centre de calcul,
  • offre un support (accueil, assistance et formation) aux utilisateurs de ces ressources,
  • réalise des prestations « à façon » dans le cadre de collaborations scientifiques autour de projets de recherche portés par des laboratoires de biologie.

Enfin, le CBiB s’efforce de rendre accessible à travers son site WEB l’ensemble des ressources (bases de données, programmes) déployées : qu’il s’agisse de ressources publiques installées sur les machines du CBiB ou de ressources développées au sein même du CBiB.



Site web : CBIB

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Filed Under: Sites

Sequence analysis tools

Posted on décembre 6, 2009 by Commentaires fermés sur Sequence analysis tools

Next-generation sequencing

MICSA A software for detecting transcription factor binding sites from NGS ChIPseq data
SVdetect A software for detecting structural rearrangements from NGS mate-pair genomic sequencing data
NG6 Storage and basic analysis of data produced by the 454 sequencer of the Sequencing and Genotyping platform
S-Mart Analysis tools box for high throughput management data: sequences produced by NGS technologies; for example, it manages RNA-Seq and ChIp-Seq data and provide many plots to visualize the data

Genome annotation

CAAT-Box Software package containing methods for the follow-up of the assembly phases and for initiating annotation during the finishing stage
MicroScope/MaGe (Re)annotation and comparative analysis of microbial genomes
Rasta-Bacteria Rapid Automated Scan for Toxins and Antitoxins in Bacteria
AGMIAL Integrated system for bacterial genome annotation

Genome visualisation

SynteBase/SynteView A tool to visualize gene order conservation in prokaryotic genomes
Autograph Interactive web server for automating and visualizing comparative genome maps
MuGeN Software package for the visual exploration of multiple annotated genome portions

DNA & Protein motifs

Dr Motifs A comprehensive portal for pattern matching and discovery.
STAN Nucleic or proteic pattern search based on SVG (String Variable Grammar)
CRISPI User-friendly web interface with many graphical tools and facilities allows extracting CRISPR, finding out CRISPR in personal sequences or calculating sequence similarity with spacers
ModuleOrganizer Detecting modules in families of transposable elements
Hectar Heterokont subcellular targeting prediction (ABiMS resource)
R’MES Finding exceptional motifs in sequences
PRIAM Enzyme-specific profiles for metabolic annotation
REPET Analysis tool for detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements (TEs)
BLASTER Analysis suite for transposable element search and annotation in large eukaryotic genome sequence but generic enough to be applied in other contexts

RNA

VARNA Interactive drawing and editing of the RNA secondary structure
Erpin A program for the detection of RNA motifs inferred from RNA sequence alignments
RNAspace Integrated environment for non-coding RNA annotation; RNAspace makes available a variety of ncRNA gene finders and ncRNA databases as well as user-friendly tools to explore computed results including comparison, visualization and edition of putative RNAs

Phylogeny

PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
TreeDyn Dynamic graphics and annotations for analyses of trees
GenePop Population genetics software package
APE Analyses of phylogenetics and evolution in R language
MLVA web service Databases of tandem repeats typing data for population studies of bacterial pathogens; tools to produce additional private or public databases
Phylogeny.fr Automated and configurable workflow for molecular phylogeny
SeaView Multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny

Miscellaneous

GenRGenS Software for generating random genomic sequences and structures
genofrag/iThos Tool for segmenting bacterial genomes into fragments of identical size for long-range PCR amplification
Gigablaster Fast parallel Blast search on specialized sequence databases
Tcoffee A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures
ADE-4 Software package for multivariate statistics, official R package since 2002
DICROPROT Analysis of circular dichroism spectra
AnTheProt Graphical user interface for protein sequence analysis and molecular graphic display (Windows systems)

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Filed Under: Genomics