Tools deployed by IFB platforms

3SRP Pipeline

(BiRD)

Analysis pipeline using Snakemake for transcriptome profiling by 3' RNA sequencing.

2 Associated keyword(s)

NGS data analysis
Transcriptomics (RNA-seq)

Conditions of use

This pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline

Specifications

Input format:

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Contact information
Visit tool home page

Contact tool support by mail
ACD Tools 2.0

(PACA-Bioinfo)

A web-server for the generic analysis of large data sets of counts

1 Associated keyword(s)

Biostatistics

Conditions of use

Gratuit

Specifications

Input format:

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Output format:

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License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
ACNUC

(PRABI-Lyon-Grenoble)

Sequence retrieval system for the nucleotide (GenBank, EMBL) and protein (UniProt) sequence databases and for many other systems following the same formats. Full description available froim the software home page.

3 Associated keyword(s)

Information and communication technology developments
Data
Databases and information systems

Conditions of use

Freely downloadable software licensed under the GNU General Public License (http://doua.prabi.fr/databases/acnuc) or on-line access through a web interafce (http://doua.prabi.fr/search/query_fam).

Specifications

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Contact information
Visit tool home page

Contact tool support by mail
ActivCollector

(AuBi)

Estimation tools design of energy expenditure and energy intake.

1 Associated keyword(s)

No relevant terms in the list above

Conditions of use

Gratuit

Specifications

Input format:

Value not provided

Output format:

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License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
ADE-4

(PRABI-Lyon-Grenoble)

R library for multivariate analysis and graphical display. Full description available from the software home page.

4 Associated keyword(s)

Biostatistics
Multivariate analysis
Ecology
Microbial ecology

Conditions of use

Freely available for download from any CRAN mirror.

Specifications

Input format:

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Output format:

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Contact information
Visit tool home page

Contact tool support by mail
AGMIAL

(MIGALE)

AGMIAL, plate-forme d’annotation de génomes microbiens. Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, Penaud S, Maguin E, Hoebeke M, Bessières P, Gibrat JF: AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res 2006, 34:3533–3545.

3 Associated keyword(s)

Genomics (DNA-seq)
Genome analysis
Structural and functional genome annotation

Conditions of use

Le logiciel peut être téléchargé gratuitement sur le site http://genome.jouy.inra.fr/agmial. Il est également possible de demander l’installation d’une instance d’AGMIAL sur les machines de la plate-forme MIGALE.

Specifications

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Contact information
Visit tool home page

Contact tool support by mail
Ant-Motifs

(AuBi)

Motifs extraction and supervised classification for proteins structure. Publications : R. Saidi, M. Maddouri, and E.M. Nguifo (2010) Protein sequences classification by means offeature extraction with substitution matrices. BMC bioinformatics, 11(1): 175. doi:10.1186/1471-2105-11-175 R. Saidi, W. Dhifli, M. Maddouri, and E.M. Nguifo. (2019) Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs. J. Comput. Biol., 26 (6), 561-571. doi:10.1089/cmb.2018.0171

2 Associated keyword(s)

Sequence analysis
Structural bioinformatics

Conditions of use

Gratuit sur http://www.isima.fr/~mephu/FILES/AntMotif/

Specifications

Input format:

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Output format:

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License(s) : Value not provided

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Contact information
Visit tool home page

Contact tool support by mail
Askomics

(GenOuest )

AskOmics is a visual SPARQL query builder for RDF database.

5 Associated keyword(s)

NGS data analysis
Integration of heterogeneous data
Knowledge representation
Ontologies
Semantic Web

Conditions of use

Free

Specifications

Input format:

Value not provided

Output format:

Value not provided

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
Aureme

(GenOuest )

The toolbox AuReMe allows for the Automatic Reconstruction of Metabolic networks based on the combination of multiple heteregeneous data and knowledge sources. Since 2016, the workflow has been made available as a Docker image to facilitate its distribution among the scientific community

4 Associated keyword(s)

Integration of heterogeneous data
System biology
Metabolic network modelling
Metabolic network analysis

Conditions of use

Free

Specifications

Input format:

Value not provided

Output format:

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License(s) : Value not provided

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Contact information
Visit tool home page

Contact tool support by mail
Autograph

(GenOuest )

AutoGRAPH is an integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.

4 Associated keyword(s)

Sequence analysis
Homology/Orthology prediction
Comparative genomics
Genome comparison

Conditions of use

Free access.

Specifications

Input format:

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Output format:

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License(s) : Value not provided

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Contact information
Visit tool home page

Contact tool support by mail
BCSearch

(RPBS)

BCSearch is a fast and flexible approach to identify linear fragments similar to a query in large collections of structures. It addresses two basic questions: Among a subset of structures, what sequences are compatible with the conformation of my query ? Are there conformations similar to my query in other proteins ? Is it observed elsewhere ? BCSearch is based on a new similarity approach, based on a Binet Cauchy (BC) kernel. The approach measures the correlation between the volumes of all the tetraedron of the query and that of a target. The similarity (BCscore) is scored between -1 and 1, where a value of 1 corresponds to the exact same conformation than the query, and -1 to the mirror conformation. Values close to 0 correspond to unrelated fragments. The BCscore is more stringent than other criteria such as the alpha carbon RMS deviation. Particularly, fragments with partly dissimilar shapes are poorly scored and consequently collections of matches are usually less noisy, which makes them better suited for the analysis of the local structure-sequence relationship. In addition, since no superimposition is required, the similarity search is very fast, making possible to mine large collections of structures.

2 Associated keyword(s)

Structural bioinformatics
Structure analysis, homologous and structural motifs discovery

Conditions of use

Online free access

Specifications

Input format:

Value not provided

Output format:

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License(s) : Value not provided

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Contact information
Visit tool home page

Contact tool support by mail
BioMAJ

(GenOuest )

BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing. The software automates the update cycle and the supervision of the locally mirrored databank repository. The software is free and released under AGPL v3 based licence.

2 Associated keyword(s)

Data
Data management and transfer

Conditions of use

Téléchargement libre : https://github.com/genouest/biomaj

Specifications

Input format:

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Output format:

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Contact information
Visit tool home page

Contact tool support by mail
BioMAJ2Galaxy

(GenOuest )

BioMAJ2Galaxy makes it possible to configure BioMAJ to automatically download some reference data, to then convert them and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers.

2 Associated keyword(s)

Data management and transfer
Databases and information systems

Conditions of use

Téléchargement libre : https://github.com/genouest/biomaj2galaxy

Specifications

Input format:

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Output format:

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Contact information
Visit tool home page

Contact tool support by mail
BioNJ

(ATGC)

Méthode de distance pour l'inférence d'arbres phylogénétiques.

3 Associated keyword(s)

Evolution and phylogeny
Molecular evolution
Genes and genomes

Conditions of use

Gratuit via le site web de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

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License(s) : Value not provided

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Contact information
Visit tool home page

Contact tool support by mail
BioShaDock

(GenOuest )

BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts deﬁned in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user deﬁned tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists.

6 Associated keyword(s)

Information and communication technology developments
Tools
Tool integration
Computing environments
Cluster
Cloud

Conditions of use

Accès libre sur docker-ui.france-bioinformatique.fr/

Specifications

Input format:

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Output format:

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License(s) : Value not provided

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Contact information
Visit tool home page

Contact tool support by mail
Cadbiom

(GenOuest )

CADBIOM is an open source modelling software. Based on Guarded transition semantic, it gives a formal framework to help the modelling of biological systems such as cell signaling network.

3 Associated keyword(s)

System biology
Regulatory network modelling
System modelling

Conditions of use

Free

Specifications

Input format:

Value not provided

Output format:

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Contact information
Visit tool home page

Contact tool support by mail
Carnac

(bilille)

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

1 Associated keyword(s)

Sequence analysis

Conditions of use

You can use Carnac via the web interface. It is also possible to download and install it locally (carnac.tar.gz and read_me). You need a C compiler.
A Windows executable is also available in this zip archive .

Specifications

Input format:

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Contact information
Visit tool home page

Contact tool support by mail
Caspo

(GenOuest )

The caspo pipeline is dedicated to automated reasoning on logical signaling networks

3 Associated keyword(s)

System biology
System modelling
Dynamic systems

Conditions of use

Free

Specifications

Input format:

Value not provided

Output format:

Value not provided

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Operating system(s): Value not provided

License(s) : Value not provided

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Contact information
Visit tool home page

Contact tool support by mail
CesGO

(GenOuest )

CeSGO offers a complete Virtual Research Environment (VRE) for Life Sciences. This VRE is based on a collaborative environment built on Wordpress and BuddyPress. It associated to the data sharing services of Owncloud and the SEEK platform. Main site : https://www.cesgo.org/en/ Collaborative platform : https://www.cesgo.org/collaboration Data management platform : https://data-access.cesgo.org Scientific data platform : https://seek.cesgo.org/

6 Associated keyword(s)

Information and communication technology developments
Tool integration
Interfaces, web portals
Data integration
Data management and transfer
Databases and information systems

Conditions of use
Value not provided

Specifications

Input format:

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Contact information
Visit tool home page

Contact tool support by mail
Clust&See

(TAGC-BCF)

Clust&See est un plug-in Cytoscape dans lequel plusieurs algorithmes de partitionnement de graphes et OCG sont implémentés. Il permet d'identifier, de visualier et d'analyser les classes de sommets obtenus. La partition obtenue est visualisée sour la forme d'un graphe quotient. Cet outil permet d'étudier en détail les liens entre sommlets, arêtes, classes et partitions.

3 Associated keyword(s)

System biology
Complex biological systems functions
Multi-layer analysis and modelling

Conditions of use

Libre sur http://tagc.univ-mrs.fr/tagc/index.php/clustnsee et sur l'App store.

Specifications

Input format:

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Output format:

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
CompPhy

(ATGC)

Serveur collaboratif de comparaison de phylogénies.

5 Associated keyword(s)

Evolution and phylogeny
Molecular evolution
Genes and genomes
Phylogenomics
Supertrees et reconciliations

Conditions of use

Gratuit via le site web de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
CRAC

(bilille)

CRAC proposes a novel way of analyzing reads that integrates genomic locations and local coverage, and delivers all above mentioned predictions in a single step. CRAC uses a double k-mer profiling approach to detect candidate mutations, indels, splice or fusion junctions in each single read.

1 Associated keyword(s)

NGS data analysis

Conditions of use

CRAC is released under a CECiLL licence (a GPL-compliant licence). You can download it and install it on your server.

Specifications

Input format:

Value not provided

Output format:

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
CRAC

(ATGC)

Méthode d'analyse de données RNA-seq.

4 Associated keyword(s)

NGS data analysis
Transcriptomics (RNA-seq)
Differential gene expression analysis
Transcripts and transcript variants analysis

Conditions of use

Gratuit via le site de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
DEPIB

(BiRD)

Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.

2 Associated keyword(s)

NGS data analysis
Transcriptomics (RNA-seq)

Conditions of use

This pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipe...

Specifications

Input format:

Value not provided

Output format:

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
Dgenies

(Genotoul-bioinfo)

D-GENIES is a standalone and WEB application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference , zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy to install open source software package (GPL) developed in Python and JavaScript.

2 Associated keyword(s)

Genome analysis
(multiple) Sequence Alignment

Conditions of use

D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is freely available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

Specifications

Input format:

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Output format:

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
DiNAMO

(bilille)

The DiNAMO software implements an exhaustive algorithm to detect over-represented IUPAC motifs in a set of DNA sequences. It has two modes: scanning mode, where all windows are parsed, or fixed-position mode, where only motifs occurring at a specific position in the sequences are taken into account. DiNAMO can be used in a variety of applications, such as ChIP-seq peak analysis for transcription factor binding sites identification, or finding motifs that induce systematic sequencing errors.

1 Associated keyword(s)

Sequence analysis

Conditions of use

Aucune

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
DroPNet

(AuBi)

Drosophila Protein Network allows the generation and analysis of protein-protein interaction (PPI) networks. This platform will help integrating user experimental data with various available PPI databases. Publication : Y. Renaud, A. Baillif, J-B. Perez, M. Agier, E. Mephu Nguifo, V. Mirouse (2012) DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. Nucleic Acids Research, 40(Web Server issue):W134-9, Oxford. doi:10.1093/nar/gks434

2 Associated keyword(s)

Bioimaging
Proteomics

Conditions of use

Gratuit sur http://dropnet.isima.fr/site/

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
e-BGO

(GenOuest )

Portail de collaboration scientifique (mise en production en 2013).

2 Associated keyword(s)

Interfaces, web portals
Databases and information systems

Conditions of use

Accès public.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
ESPript/ENDscript

(PRABI-Lyon-Gerland)

Value not provided

5 Associated keyword(s)

Sequence analysis
(multiple) Sequence Alignment
Sequence motif discovery
Structural bioinformatics
Structure analysis, homologous and structural motifs discovery

Conditions of use

http://espript.ibcp.fr et http://endscript.ibcp.fr

Le serveur ESPript/ENDscript est accessible gratuitement, via Internet et sans enregistrement, à la communauté scientifique pour un usage académique.

Specifications

Input format:

Value not provided

Output format:

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Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
FastME

(ATGC)

Méthode de distance pour l'inférence d'arbres phylogénétiques.

3 Associated keyword(s)

Evolution and phylogeny
Molecular evolution
Genes and genomes

Conditions of use

Gratuit via le site web de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
fpocket

(RPBS)

fpocket is a very fast, open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program, and from now as a web server too.

2 Associated keyword(s)

Structural bioinformatics
Structural property prediction

Conditions of use

Online free access.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
Frog2

(RPBS)

Frog is intended to generate 3D for drugs, usually described using a 1D or 2D representation. Frog performs isomer identification from ambiguous compound description. Frog is able to generate multi-conformations per isomer.

2 Associated keyword(s)

Structural bioinformatics
Structural property prediction

Conditions of use

Online free access

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
GalaxEast

(BiGEst)

The objective of GalaxEast (http://www.galaxeast.fr) is to provide a reliable public Galaxy instance, with guaranteed availability and accessibility. GalaxEast offers a catalogue of about a hundred tools, mainly for handling of sequencing data (ChIP-seq, RNA-seq and DNAseq) high speed. The addition of proteomic and spectroscopy data analysis tools is planned for 2014. The tools come from both the official Galaxy toolshed and the developments of bioinformaticians from the local community. The new tools will be made available in the platform toolshed. The platform has a wiki that allows users to find documentation and request the addition of new tools and genomes.

1 Associated keyword(s)

NGS data analysis

Conditions of use

Open access for the French academic research community.
Access facilitated via rapid connexions (eg : Osiris, Renater)

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
Galaxy (piloté par Sigenae)

(Genotoul-bioinfo)

Galaxy is a workbench available for biologists from Sigenae Platform. Galaxy objectives are: Make bioinfo Linux tools accessible to biogists. Hide the complexity of the infrastructure. Allow creation, execution and sharing of workflows.

5 Associated keyword(s)

NGS data analysis
Genomics (DNA-seq)
Transcriptomics (RNA-seq)
Variant calling
Metagenomics, metatranscriptomics

Conditions of use

Available on a web site with login and password.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
Galaxy@CBiB

(CBiB)

Galaxy analysis server. Bioinformatics tools made available on the Toolshed: 400 tested bricks.

2 Associated keyword(s)

NGS data analysis
Sequence analysis

Conditions of use

Free web access, possibility of access to supplementary storage

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
GATB

(GenOuest )

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS datasets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

10 Associated keyword(s)

NGS data analysis
Methodology
Genome and transcriptome assembly
Read mapping
Variant calling
Exomes
Whole genomes
Metagenomics, metatranscriptomics
Sequence analysis
Sequence algorithmics

Conditions of use

Freely available.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
Geno3D@

(PRABI-Lyon-Gerland)

Modélisation par homologie automatisée de la structure tridimensionnelle des protéines.

4 Associated keyword(s)

Structural bioinformatics
Structure analysis, homologous and structural motifs discovery
Structural property prediction
Structure comparative and de novo modelling

Conditions of use

https://geno3d-prabi.ibcp.fr (depuis février 2001).

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
GIGWA

(South Green)

Value not provided

6 Associated keyword(s)

Genomics (DNA-seq)
Variant calling
Tool integration
Interoperability
Interfaces, web portals
Databases and information systems

Conditions of use

Publique

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
GO-Docker

(GenOuest )

It is a cluster management tool using Docker as execution/isolation system. The software does not manage however itself the dispatch of the commands on the remote nodes. For this, it integrates with container management tools (Docker Swarm, Apache Mesos, ...)

4 Associated keyword(s)

Information and communication technology developments
Computing environments
Cluster
Cloud

Conditions of use

Téléchargement libre : http://www.genouest.org/godocker/index.html

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
GO2Pub

(GenOuest )

GO2PUB to automatically enrich PubMed queries with gene names, symbols and synonyms annotated by a GO term of interest or one of its descendants

6 Associated keyword(s)

Integration of heterogeneous data
Ontologies
Information and communication technology developments
Data
Data integration
Databases and information systems

Conditions of use

Accès libre

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
GoArrays

(AuBi)

Microarray probe design application. It enables the design of specific probes of each gene in an entire genome, with an original approach. The use of specific microarray technology requires a very detailed attention for the design of specific probes spotted on the solid phase. These problems are far from being commonplace since they refer to complex physicochemical constraints. We propose a new approach to design oligonucleotides which combines good specificity with a potentially high sensitivity. This approach is original in the biological point of view as far as in the algorithmic point of view, and is particularly adapted when dealing with a complex target mixture (where it’s difficult to find specific sequences fo all genes). Publication : Rimour, S., D. Hill, C. Militon, and P. Peyret (2005) GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics (Oxford, England) 21:1094-1103. doi:10.1093/bioinformatics/bti112

1 Associated keyword(s)

NGS data analysis

Conditions of use

Gratuit sur http://g2im.u-clermont1.fr/serimour/goarrays.html

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Hex

(MBI)

Ab initio rigid body protein-protein docking.

2 Associated keyword(s)

Structural bioinformatics
Structural property prediction

Conditions of use

Free licence for academic use

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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HexServer

(MBI)

Ab initio rigid body protein-protein docking using GPU.

2 Associated keyword(s)

Structural bioinformatics
Structural property prediction

Conditions of use

Free service: no login or registration required

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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HHalign-Kbest

(RPBS)

HHalign-Kbest is useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.

2 Associated keyword(s)

Structural bioinformatics
Structure comparative and de novo modelling

Conditions of use

Online free access

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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HiSpOD

(AuBi)

Software dedicated for the microbial ecology and environmental studies. The software use individual nucleic sequences or consensus sequences produced by multiple alignments to design degenerate probes in order to target gene families covering many exhaustive formatted database dedicated to microbial ecology containing about 10 million coding sequences (CDS) and their putative 5’ and 3’ untranslated regions (UTR). Potential cross-hybridizations identified by the program are clustered and results are organized in order to simplifyuser interpretation. Publications : Dugat-Bony E., Missaoui M., Peyretaillade E. , Biderre-Petit C. , Bouzid O., Gouinaud C. , Hill D. , and Peyret P. (2011) HiSpOD: probe design for functional DNA microarrays. Bioinformatics (Oxford, England) 27:641-648. doi:10.1093/bioinformatics/btq712 Parisot N., Peyretaillade E., Dugat-Bony E., Denonfoux J., Mahul A., and Peyret P. (2016) Probe Design Strategies for Oligonucleotide Microarrays. Methods in Molecular Biology, 1368: 67-82. doi: 10.1007/978-1-4939-3136-1_6

2 Associated keyword(s)

Sequence analysis
Genomics: Chips

Conditions of use

Gratuit sur http://g2im.u-clermont1.fr/hispod/index.php

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Integron Finder

(Pasteur HUB)

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (galaxy), or by command line (IntegronFinder on github). Integrons are major genetic element, notorious for their major implication in the spread of antibiotic resistance genes. More generally, integrons are gene-capturing device, whose broader evolutionary role remains poorly understood. IntegronFinder is able to detect with high accuracy integron in DNA sequences. It is accurate because it combines the use of HMM profiles for the detection of the essential protein, the site-specific integron integrase, and the use of Covariance Models for the detection of the recombination site, the attC site. IntegronFinder can also annotate gene cassettes (CDS nearby attC sites) using Resfams, a database of HMM profiles aiming at annotating antibiotic resistance genes. This database is provided but the user can add any other HMM profiles database of its own interest.

2 Associated keyword(s)

Sequence annotation
Sequence motif discovery

Conditions of use

Integron_Finder is released under the GPLv3 license and is available here: https://github.com/gem-pasteur/Integron_Finder

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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InterEvDock2

(RPBS)

InterEvDock is a server for protein docking running the InterEvScore potential specifically designed to integrate evolutionary information in the docking process. The InterEvScore potential was developed for heteromeric protein interfaces and combines a residue-based multi-body statistical potential with evolutionary information derived from the multiple sequence alignments of each partner in the complex.

2 Associated keyword(s)

Structural bioinformatics
Structure comparative and de novo modelling

Conditions of use

Online free access

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Interface web blast

(Genotoul-bioinfo)

Web blast interface

1 Associated keyword(s)

Sequence analysis

Conditions of use

Available on the web site.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Interface web Emboss

(Genotoul-bioinfo)

emboss tools interface.

1 Associated keyword(s)

Sequence analysis

Conditions of use

Site web

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Jvenn

(Genotoul-bioinfo)

A javascript plugin for venn diagrams. A demo is available here: http://bioinfo.genotoul.fr/jvenn/example.html

1 Associated keyword(s)

Interfaces, web portals

Conditions of use

The software package is available under the GNU General Public License (GPL) and can be downloaded from the gitlab forgemia : https://forgemia.inra.fr/genotoul-bioinfo/jvenn.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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KASpOD

(AuBi)

Program for designing signature sequences for various applications including in phylogenetic or functional microarray experiments. Publication: Parisot, N., J. Denonfoux, E. Dugat-Bony, P. Peyret, and E. Peyretaillade (2012) KASpOD--a web service for highly specific and explorative oligonucleotide design. Bioinformatics (Oxford, England) 28:3161-3162.doi:10.1093/bioinformatics/bts597

2 Associated keyword(s)

Sequence analysis
Genomics: Chips

Conditions of use

Gratuit sur http://g2im.u-clermont1.fr/kaspod/

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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Kpax

(MBI)

Fast protein structure alignment (pairwise, multiple, flexible) and database search (e.g. CATH, SCOP, ECOD, Pfam).

2 Associated keyword(s)

Structure analysis, homologous and structural motifs discovery
Structure comparative and de novo modelling

Conditions of use

No-cost licence for academic use.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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leBiBI

(PRABI-Lyon-Grenoble)

Online system (associated with various sequence databases) devoted to bacterial taxonomic identification.

2 Associated keyword(s)

NGS data analysis
Metagenomics, metatranscriptomics

Conditions of use

Free online access.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Logol

(GenOuest )

Langage pour la recherche de motifs complexes. Interface web évoluée et téléchargement possible. La ressource a été mise en ligne en 2013 pour une première phase d’utilisation interne pour finaliser les développements et aboutir à un système stable.

2 Associated keyword(s)

Sequence analysis
Sequence motif discovery

Conditions of use

Utilisation interne.

Accès libre.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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LoRDEC

(ATGC)

Logiciel de correction des longs reads.

5 Associated keyword(s)

NGS data analysis
Methodology
Read mapping
Genomics (DNA-seq)
Transcriptomics (RNA-seq)

Conditions of use

Gratuit depuis le site web de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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LSD

(ATGC)

LEAST-SQUARES METHODS TO ESTIMATE RATES AND DATES FROM SERIAL PHYLOGENIES

1 Associated keyword(s)

Speciation dating

Conditions of use

Gratuit via le site web de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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macsyfinder

(Pasteur HUB)

Detection of macromolecular systems in protein datasets using systems modelling and similarity search. MacSyFinder is a program to model and detect macromolecular systems, genetic pathways in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection. Criteria for systems detection include component content (quorum), and genomic co-localization. Each component corresponds to a hidden Markov model (HMM) protein profile to perform homology searches with the program Hmmer . Homepage : https://github.com/gem-pasteur/macsyfinder

2 Associated keyword(s)

Sequence analysis
Sequence annotation

Conditions of use

freely available (GPLv2)

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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MEMHDX

(Pasteur HUB)

MEMHDX allows users to perfom an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure. ref: Véronique Hourdel, Stevenn Volant, Darragh P. O’Brien, Alexandre Chenal, Julia Chamot-Rooke, Marie-Agnès Dillies, Sébastien Brier; MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets. Bioinformatics 2016; 32 (22): 3413-3419. doi: 10.1093/bioinformatics/btw420

2 Associated keyword(s)

Biostatistics
Interfaces, web portals

Conditions of use

MEMHDX is freely available as a web tool at http://memhdx.c3bi.pasteur.fr/

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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MICADo

(CBiB)

Mutation discovery in target PacBio cancer data with an alignment free method.

3 Associated keyword(s)

NGS data analysis
Methodology
Variant calling

Conditions of use

Public.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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MicroAnnot

(AuBi)

Pipeline dedicated to microsporidian genome annotation under Galaxy. Not already published.

1 Associated keyword(s)

Sequence analysis

Conditions of use

Gratuit sur http://galaxy01.calcul.crri.fr/

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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MicroScope

(MicroScope)

Located at Genoscope (CEA sequencing center for environmental genomics), the LABGeM bioinformatics team has developed MicroScope, a web-based platform for prokaryotic genome analysis and expert functional annotation. MicroScope combines tools and graphical interfaces to analyze genomes and to perform manual curation of gene function in a comparative and metabolic context. This platform provides data from completed and ongoing genome projects together with post-genomic experiments (i.e. transcriptomics, re-sequencing of evolved strains) allowing users to improve the understanding of gene functions. Expert annotations are continuously gathered in the MicroScope database contributing to the improvement of the quality of microbial genome annotations, and thus to the predicted metabolic networks. MicroScope can be used as a community resource for comparative analysis and annotation of publicly available genomes but also as a private resource with restricted access rights on genomic data. In addition, we regularly hold professional trainings sessions on the use of MicroScope platform.

33 Associated keyword(s)

NGS data analysis
Read mapping
Genomics (DNA-seq)
Genome analysis
Structural and functional genome annotation
Transcriptomics (RNA-seq)
Differential gene expression analysis
Variant calling
Whole genomes
Metagenomics, metatranscriptomics
Sequence analysis
Sequence algorithmics
(multiple) Sequence Alignment
Sequence annotation
Sequence motif discovery
Homology/Orthology prediction
System biology
Metabolic network modelling
Tools
Tool integration
Interoperability
Interfaces, web portals
Workflows developments
Data
Data integration
Data management and transfer
Databases and information systems
Computing environments
Cluster
Parallelisation
Comparative genomics
Genome comparison
Comparison of functional and regulatory pathways

Conditions of use

Free for academics.

Sales quote available on demand for non-academics

Service features:

Microbial genome annotation (complete, WGS or metagenome-assembled genomes)

Comparative genomics and pangenomics

Function and biological process predictions

Metabolic network reconstruction

Analysis of transcriptomics data

Variant calling of evolved strains

Technical support

Trainings on prokaryotic genome annotation and on the curation of metabolic networks

More details here.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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microSysMics

(BiRD)

This workflow provides an automated microbiome data analysis, starting with sequenced taxonomic markers (such as 16SrRNA) and using the standard QIIME2 toolbox to produce an abundance table and preliminary diversity, phylogeny and taxonomy analysis.

1 Associated keyword(s)

Metagenomics, metatranscriptomics

Conditions of use

This pipeline is public, the source code is available here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/microSysMics

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Minia

(GenOuest )

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

5 Associated keyword(s)

NGS data analysis
Methodology
Genome and transcriptome assembly
Sequence analysis
Sequence algorithmics

Conditions of use

Free

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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MIX

(CBiB)

Finishing of genome assemblies

2 Associated keyword(s)

NGS data analysis
Methodology

Conditions of use

Free web access

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

Contact tool support by mail
mixkernel

(Genotoul-bioinfo)

Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package.

1 Associated keyword(s)

Integration of heterogeneous data

Conditions of use

mixKernel is freely available on CRAN. It is fully compatible with the mixOmics package and a tutorial describing the approach can be found on mixOmics web site.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Mobyle

(Pasteur HUB)

Mobyle is a framework and web portal specifically aimed at the integration of bioinformatics software and databanks. Mobyle is the successor of Pise and the RPBS server, previous systems that provided web environments to define and execute bioinformatics analyses. Functionalities: data reusability: the tagging of the user data facilitates the reuse of input values or results between different programs. automatic data validation and format conversion: the description of the expected data and their format allows to verify and convert input values if necessary. service discovery and workflow authoring assistance: services are provided through a searchable menu; furthermore, type compatibility mechanisms between results and potential program inputs let users either interactively pipe tasks or build complete workflows before to run them. Based on extensive user studies, we developed the end-user interface as a Web Portal that provides a global and integrated view of all the elements needed to perform analyses, such as the available programs, the submitted jobs and the data of interest. References: Bertrand Néron, Hervé Ménager, Corinne Maufrais, Nicolas Joly, Julien Maupetit, Sébastien Letort, Sébastien Carrere, Pierre Tuffery, and Catherine Letondal Mobyle: a new full web bioinformatics framework Bioinformatics (2009); 25 (22): 3005-3011. doi:10.1093/bioinformatics/btp493.

9 Associated keyword(s)

Information and communication technology developments
Tools
Tool integration
Interoperability
Interfaces, web portals
Data
Data integration
Computing environments
Cluster

Conditions of use

The Mobyle framework is developped under the GPLv2 license.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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MPscan

(ATGC)

Méthode de mapping de reads sur un génome sans index.

3 Associated keyword(s)

NGS data analysis
Methodology
Read mapping

Conditions of use

Gratuit via le site web de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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MSDA

(BiGEst)

A software suite and databases for the interpretation of data from proteomic analyses by mass spectrometry (database search tools, de novo sequencing pipeline, extraction of protein functional annotations, extraction of spectra based on spectral quality criteria,...). Carapito et al. Proteomics. 2014 14:1014-1019.

1 Associated keyword(s)

Proteomics

Conditions of use

Free Web access

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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MTiAutoDock/MTiOpenScreen

(RPBS)

MTiAutoDock and MTiOpenScreen are two services dedicated to small molecule docking and chemical library virtual screening.

4 Associated keyword(s)

Structural bioinformatics
Virtual screening
Small chemical compounds libraries, 2D/3D, ADME/tox
Structure-based screening

Conditions of use

Online free access

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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NG6

(Genotoul-bioinfo)

The platform works in tight collaboration with the GeT sequencing platform for the management and the analysis of data produced by their Roche 454 and Illumina HiSeq sequencers. NG6 is an extensible sequencing provider oriented LIMS. It includes read quality control and first level analysis processes which ease the data validation made jointly by the sequencing facility staff ant the end-users. It provides a secured user-friendly interface to visualize and download the raw sequences files and the analysis results.

2 Associated keyword(s)

Interfaces, web portals
Data management and transfer

Conditions of use

The NG6 code is freely available on the gitlab formia : https://forgemia.inra.fr/genotoul-bioinfo/ng6. To ease the installation, the package and all its dependencies are also available as a virtual machine. Installing and maintaining the system would require expertise in Linux system administration.
Available by the web site for users

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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NGS-QC Generator

(BiGEst)

ANALYSIS OF THE DATA NGS - QUALITY CONTROL OF READINGS Universal quality control system for ChIP-seq and NGS 'enrichment-based' data (www.ngs-qc.org). The NGS-QC database hosts QC descriptors for 6066 publicly available data sets. Mendoza-Parra et al. A quality control system for profiles obtained by ChIP sequencing Nucleic Acids Res. 2013 41:e196. NB : content continuously updated to maintain coverage of all public data sets

1 Associated keyword(s)

NGS data analysis

Conditions of use

Free Web access for the academic research community. Premium access is also available on request.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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NPS@

(PRABI-Lyon-Gerland)

Serveur intégré d’analyse de séquences des protéines.

8 Associated keyword(s)

Sequence analysis
Sequence algorithmics
(multiple) Sequence Alignment
Sequence annotation
Sequence motif discovery
Homology/Orthology prediction
Structural bioinformatics
Structural property prediction

Conditions of use

https://npsa-prabi.ibcp.fr (depuis avril 1998).

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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Nucbase

(AuBi)

Program designed to make an exhaustive search for sequence matches and to align short sequence reads from large nucleic acid databases to genomes or input sequences. Publication : Dufourt, J., P. Pouchin, P. Peyret, E. Brasset, and C. Vaury (2013) NucBase, an easy to use read mapper for small RNAs. Mobile DNA 4(1):1.doi:10.1186/1759-8753-4-1

1 Associated keyword(s)

No relevant terms in the list above

Conditions of use

Gratuit sur https://grr.gred-clermont.fr/nucbase

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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NucleusJ

(AuBi)

Plugin for 3D image analysis. - Publication : Poulet, A., I. Arganda-Carreras, D. Legland, A. V. Probst, P. Andrey, and C. Tatout (2015) NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics (Oxford, England) 31(7):1144-1146. doi:10.1093/bioinformatics/btu774

1 Associated keyword(s)

No relevant terms in the list above

Conditions of use

Gratuit sur http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_pl...

Wiki ImageJ requis.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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OCG

(TAGC-BCF)

OCG est un algorithme d'analyse de grapghe qui identifie des classes chevauchantes de sommlets par optimisation de la modularité de l'ensemble des classes.

2 Associated keyword(s)

Complex biological systems functions
Multi-layer analysis and modelling

Conditions of use

Téléchargement du code source à partir de http://tagc.univ-mrs.fr/tagc/index.php/research/network-bioinformatics/c...

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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ORDO

(Orphanet)

Orphanet Rare Disease Ontology: Nomenclature, classifications and scientific data on rare diseases exploitable in an ontological form in OWL format. Elaborated in partnership with the European Bioinformatics Institute (EBI ; Contact Helen Parkinson). Available since January 2014.

13 Associated keyword(s)

Machine learning
Knowledge extraction
Integration of heterogeneous data
Knowledge representation
Ontologies
Semantic Web
Data curation
Information and communication technology developments
Tools
Tool integration
Data
Data integration
Databases and information systems

Conditions of use

Downloadable and freely accessible via Orphadata.org,
Downloadable and usable via Bioportal.

Availability of a sparql EndPoint.

Specifications

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License(s) : Value not provided

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OrthoInspector

(BiGEst)

Rapid detection of orthology and inparalogy relations. Linard B, et al. OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics. 2011 Jan 10;12:11.

1 Associated keyword(s)

Sequence analysis

Conditions of use

http://bioinfo-bistro.fr/orthoinspector/

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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PANAM

(AuBi)

PANAM makes it possible to analyse a large dataset of 18S rRNA in a simple and rapid way. It assigns taxonomy to reads generated by next generation sequencing technologies or to near-full-length sequences, and permits to define environmental clades. A readme file text that contains instructions to set up PANAM is available in the package (Taib et al. 2013). Publication : Taib, N., J. F. Mangot, Domaizon, I., Bronner G., and Debroas D. (2013) Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity. PloS one 8:e58950.doi:10.1371/journal.pone.0058950

1 Associated keyword(s)

No relevant terms in the list above

Conditions of use

Gratuit sur https://code.google.com/p/panam-phylogenetic-annotation/

Specifications

Input format:

Value not provided

Output format:

Value not provided

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License(s) : Value not provided

Version : Value not provided

Contact information
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PanGeneHome

(AuBi)

PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. Several standalone tools (e.g. PGAP, PANNOTATOR, PanGP, Roary and BPGA) and web servers (e.g. Panseq, PGAT and PanWeb) dedicated to pangenome analysis have been developed recently and offer the possibility to compute pangenome analysis for genomes provided by a user. For all these tools and servers, users have to collect genomes and manage to run the tools, which implies a significant effort on the user side. To tackle this problem, we developped PanGeneHome, the only web site offering pre-computed pangenome analysis with up-to-date and large scale data. PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest, the analysis being precomputed and available for 615 taxa, covering 182 species and 49 orders. Considering the fast growing number of microbial genomes, the PanGeneHome tool will need to be updated regularly. Publication: Loiseau C., Hatte V., Andrieu C., Barlet L., Cologne A., De Oliveira R., Ferrato-Berberian L., Gardon H., Lauber D., Molinier M., Monnerie S., N 'Gou K., Penaud B., Pereira O., Picarle J., Septier A., Mahul A., Charvy J.-C. and Enault F. (2018) Journal of Bioinformatics, Computational and Systems Biology. arXiv:1805.05597

3 Associated keyword(s)

Sequence analysis
Evolution and phylogeny
Comparative genomics

Conditions of use

Gratuit

Specifications

Input format:

Value not provided

Output format:

Value not provided

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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PEP-FOLD

(RPBS)

PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences. This method, based on structural alphabet SA letters to describe the conformations of four consecutive residues, couples the predicted series of SA letters to a greedy algorithm and a coarse-grained force field.

2 Associated keyword(s)

Structural bioinformatics
Structure comparative and de novo modelling

Conditions of use

Online free access

Specifications

Input format:

Value not provided

Output format:

Value not provided

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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PepPSY

(GenOuest )

PepPSy has been developed as a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein and curators to quickly look at available transcriptomics/proteomics data for a list of proteins.

3 Associated keyword(s)

Homology/Orthology prediction
Comparison of functional and regulatory pathways
Proteogenomics

Conditions of use

Accès libre

Specifications

Input format:

Value not provided

Output format:

Value not provided

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License(s) : Value not provided

Version : Value not provided

Contact information
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PepTeam

(CBiB)

PepTeam is a tool for biomarker discovery from the analysis of in-vivo screened repertoire of phage displayed libraries that has been sequenced by NGS.

3 Associated keyword(s)

Sequence analysis
Sequence algorithmics
Sequence motif discovery

Conditions of use

Through CBiB Galaxy interface.

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
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PhylArray

(AuBi)

Program for designing oligonucleotide probes (from 16S rRNA) for use in phylogenetic microarray experiments. Publication : Militon, C., S. Rimour, M. Missaoui, C. Biderre, V. Barra, D. Hill, A. Mone, G. Gagne, H. Meier, E. Peyretaillade, and P. Peyret (2007) PhylArray: phylogenetic probe design algorithm for microarray. Bioinformatics (Oxford, England) 23:2550-2557. doi:10.1093/bioinformatics/btm392

1 Associated keyword(s)

No relevant terms in the list above

Conditions of use

Gratuit sur http://g2im.u-clermont1.fr/serimour/phylarray/

Specifications

Input format:

Value not provided

Output format:

Value not provided

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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phylogeny.fr

(ATGC)

Pipeline d'analyse phylogénétique.

3 Associated keyword(s)

Evolution and phylogeny
Molecular evolution
Genes and genomes

Conditions of use

Gratuit via le site web de la plateforme.

Specifications

Input format:

Value not provided

Output format:

Value not provided

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Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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Phylogeny.fr/ Blast-Explorer

(PACA-Bioinfo)

Robust Phylogenetic Analysis For The Non-Specialist

3 Associated keyword(s)

Sequence analysis
Evolution and phylogeny
Comparative genomics

Conditions of use

Gratuit

Specifications

Input format:

Value not provided

Output format:

Value not provided

Application type(s): Value not provided

Operating system(s): Value not provided

License(s) : Value not provided

Version : Value not provided

Contact information
Visit tool home page

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PhyML

Tools deployed by IFB platforms

3SRP Pipeline

ACD Tools 2.0

ACNUC

ActivCollector

ADE-4

AGMIAL

Ant-Motifs

Askomics

Aureme

Autograph

BCSearch

BioMAJ

BioMAJ2Galaxy

BioNJ

BioShaDock

Cadbiom

Carnac

Caspo

CesGO

Clust&See

CompPhy

CRAC

CRAC

DEPIB

Dgenies

DiNAMO

DroPNet

e-BGO

ESPript/ENDscript

FastME

fpocket

Frog2

GalaxEast

Galaxy (piloté par Sigenae)

Galaxy@CBiB

GATB

Geno3D@

GIGWA

GO-Docker

GO2Pub

GoArrays

Hex

HexServer

HHalign-Kbest

HiSpOD

Integron Finder

InterEvDock2

Interface web blast

Interface web Emboss

Jvenn

KASpOD

Kpax

leBiBI

Logol

LoRDEC

LSD

macsyfinder

MEMHDX

MICADo

MicroAnnot

MicroScope

microSysMics

Minia

MIX

mixkernel

Mobyle

MPscan

MSDA

MTiAutoDock/MTiOpenScreen

NG6

NGS-QC Generator

NPS@

Nucbase

NucleusJ

OCG

ORDO

OrthoInspector

PANAM

PanGeneHome