Archive for décembre, 2009

Databases

Posted on décembre 26, 2009 by Commentaires fermés

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

Proteomics

Posted on décembre 25, 2009 by Commentaires fermés

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 Commentaires fermés

logo_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

Filed Under: Sites

PRABI

Posted on décembre 8, 2009 by Commentaires fermés

logoprabi_small209

The PRABI is the Rhône-Alpes Bioinformatics Center, a RIO platform of the Rhône-Alpes Genopole. It gathers many research teams that develop new biological modeling using mathematics and computer sciences. The PRABI provides to the national and international community the computer tools that result from these researches. Moreover some « classical » tools of bioinformatics are also available. However it is not the aim of PRABI to compete with big international centers (as EBI, NCBI, …) on which a much larger collection of tools can be found.

The PRABI expects to be an exchange tool between biologists and bioinformatic researchers. This site aims at presenting the databases and computational tools available through the PRABI for biology and health research.

Rhone-Alpes BioInformatics Center

The Rhone-Alpes BioInformatics Center is a platform gathering 11 research teams spread on 4 different sites. the PRABI has research, service and training activities in a large number of bioinformatics and biostatistics fields.



Web site : PRABI

Filed Under: Platforms

BIPS Strasbourg

Posted on décembre 8, 2009 by Commentaires fermés

The IGBMC Bioinformatics Platform is a high-throughput platform for comparative and structural genomics.
Its goal is to:
collect, maintain and deliver to the scientific community a wide range of bioinformatics resources addressing biological issues from studies of normal or pathological cells and genes to drug discovery.
develop innovative solutions and participate actively in local, regional, national and international scientific programs.
diffuse the software and databases developped by the Laboratoire de Bio-informatique et Génomique Intégratives, including analysis tools for high throughput functional or structural genomics and integrative biological studies.
share and diffuse its knowledge and expertise by organising and participating in conferences and educational courses.
The platform is accessible for external laboratories at the local, regional, national and international levels.
The Strasbourg Bioinformatics Platform was identified in 2003 as Plate-forme Nationale RIO and Génopôle Grand-Est – « from gene to drug ».
In order to meet at best the requirements of its users, partners and collaborators, the platform initiated in january 2005 a Quality Managenent System inspired from the ISO9001:2000 norm.

logo-IGBMC

The IGBMC Bioinformatics Platform is a high-throughput platform for comparative and structural genomics.

Its goal is to:

  • collect, maintain and deliver to the scientific community a wide range of bioinformatics resources addressing biological issues from studies of normal or pathological cells and genes to drug discovery.
  • develop innovative solutions and participate actively in local, regional, national and international scientific programs.
  • diffuse the software and databases developped by the Laboratoire de Bio-informatique et Génomique Intégratives, including analysis tools for high throughput functional or structural genomics and integrative biological studies.
  • share and diffuse its knowledge and expertise by organising and participating in conferences and educational courses.

The platform is accessible for external laboratories at the local, regional, national and international levels.

In order to meet at best the requirements of its users, partners and collaborators, the platform initiated in january 2005 a Quality Managenent System inspired from the ISO9001:2000 norm.


Site web : BIPS

Filed Under: Sites

RNAspace

Posted on décembre 6, 2009 by Commentaires fermés

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. This service is provided by GenoToul.
The increasing number of ncRNA discovered since 2000 and the lack of user friendly tools for finding and annotating them, have made necessary to propose to biologists an in silico environment allowing structural and functional annotations of these molecules with regard to available protein genes annotation environments.

RNAspace home page

RNAspace home page


Web site : RNAspace

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Filed Under: Platforms

GenOuest

Posted on décembre 6, 2009 by Commentaires fermés

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

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

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

Structural Bioinformatics

Posted on décembre 6, 2009 by Commentaires fermés

A large number of tools are provided by ReNaBi’s platforms.

Docking@Grid Conformational Sampling and Docking on Grids
FROST Fold recognition (threading) program
OSS-HMM Protein secondary structure prediction program
KAKSI Protein secondary structure assignment program
VAST 3D structure comparison program
NPS@ Web tools for protein structure analysis
Geno3D Automatic modelling of protein 3D structure
SOPMA Prediction of secondary structure of proteins
MLRC Prediction of secondary structure of proteins
DPM Prediction of secondary structure of proteins
SUMO Sites detection in proteins
ESPript/ENDscript Extracting and rendering sequence and 3D information from atomic structures of proteins
SOPM Prediction of secondary structure of proteins
HCA Hydrophobic Cluster Analysis

Many other tools are available. Here is a listing classified according to 4 categories :

Tertiary Structure

  • 3D structures superimposition (NPS@) available at the PRABI
  • ATOME available at Montpellier: @utomatic Threading Optimisation Modelling & Evaluation
  • CaspR available at Marseille: An automated approach for molecular replacement
  • COSA Pasteur Paris Clustal ouput structural analysis
  • COUDES online RPBS web server for beta-turn prediction
  • ElNémo: Marseille The Web-interface to The Elastic Network Model, a fast and simple tool to compute the low frequency normal modes of a protein
  • ESAP: MIG Jouy Prediction of protein loop conformation
  • Geno3D : PRABI Automatic molecular modeling
  • IMGT/StructuralQuery: Montpellier Retrieval of IMGT/3Dstructure-DB entries using domain type and/or position structural criteria
  • KinDOCK server : Montpellier Ligand Transposition Server
  • LocPred online: RPBS Local structure prediction
  • PAT server: PAT (Protein Analysis Toolkit) Montpellier toolkit to facilitate the combination of different processing tools for more complex protein analyses
  • PPG online: RPBS Protein Picture Generator
  • SA-Search online : RPBS search for 3D fragments similar to (fragments of) a query structure
  • SCit online: SCit RPBS Tools for protein side chain conformation analysis and editing
  • Small compounds: RPBS project involving the screening of databases of small chemical compounds
  • SuMo : Surfing the Molecules – Search for similar 3D sites in proteins
  • WLoop online: RPBS predict protein loop backbone structures from their sequences and their flank backbone structures
  • XmMol: RPBS desktop macromolecular visualization and modeling tool

Secondary Structure

  • Dicroprot: a single package most of the methods designed for the estimation of protein sequence secondary structure derivation from circular dichroism experiments
  • Gor IV: (MIG) method for predicting protein secondary structure from amino acid sequence
  • HCA online: Hydrophobic cluster analysis
  • PAT server: toolkit to facilitate the combination of different processing tools for more complex protein analyses
  • sspred toolkit: Secondary structure prediction
  • Simpa: MIG Jouy protein secundary structure prediction based on the « nearest-neighbor » notion

Cristallography

  • SAmBA online: Marseille, Interactively computes the experimental protocol corresponding to your combination of variables and states

NMR Tools

  • CINDY: Graphical NMR assignment software
  • CROWD:
  • GIFA: NMR processing program which includes many signal processing methods, such as Maximum Entropy, Linear Prediction, automatic Phasing, line fiting, base line correction…
  • RESCUE: An artificial neural network tool for the NMR spectral assignment of proteins

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