Author Archive

BIPS Strasbourg

Posted on décembre 8, 2009 by Commentaires fermés sur BIPS Strasbourg

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 sur RNAspace

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

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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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

Structural Bioinformatics

Posted on décembre 6, 2009 by Commentaires fermés sur Structural Bioinformatics

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

Teaching

Posted on décembre 6, 2009 by Commentaires fermés sur Teaching

Many teaching sessions are proposed each year by ReNaBi members, here are a few links about short courses suitable for continuing education :

 

 


 

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Filed Under: Teaching

Transcriptomics

Posted on décembre 6, 2009 by Commentaires fermés sur Transcriptomics

Transcriptomic tools provided by ReNaBi platforms.

GLAD A software for DNA copy number analysis in CGH arrays
MANOR A software for CGH array normalisation
VAMP An interface for visualisation of molecular profiles and their analysis
CAPweb A web tool for managing array CGH projects and analysing data
MAIA A software for two-color microarray image analysis
ITALICS A software for DNA copy number analysis in Affymetrix SNP arrays
GenoScript/Genoscape Integrated environment for microarray experiments, designed for collecting, storing and querying transcriptomic data; Genoscape is a Cytoscape plug-in that visually integrates gene expression data sets and KEGG pathways
MadTools Set of tools to facilitate the data storage, analysis and annotation obtained by the DNA microarray technology.

Additional tools, provided by transcriptomic platforms.

Biopuces (Toulouse) Platform Biopuces is one of 6 platforms of the Génopole Toulouse Midi Pyrenées. Our two main activities are : 1) service in all stages of transcriptome experiment for public and private laboratories; 2) research and development in transcriptome technics and data treatment.
ENS transcriptome platform (Paris) The ENS platform contributes to microarray technology diffusion in France and Europe among the scientific community by distributing DNA microarrays, training users, granting access to tools and devices, and collaborating with users through projects involving microarray hybridization and/or analysis.
Mediante – Microarray open source database An open-access oligonucleotide and bioinformatics resource for microarray analysis of the human and mouse transcriptomes
Nantes microarrays facility One goal of the facility is to develop, improve and offer the whole savoir-faire in molecular biology and informatics, necessary for conception and interpretation of DNA chips. It offers an assistance and service in the experimental design, and with wet-lab and dry-lab (data analysis) procedures. The aim is always to rapidly transfer the savoir-faire and expertise to the user research teams.

Filed Under: Transcriptomics

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