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Tools

Tools are in free access Public access or restricted access Registered access

They run on the web, unix or both.

Tools in restricted access can use unpublished data.


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Full List(17)

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BLAST+ NCBI 2.2.29
  • Public BLAST using ViroBLAST interface.
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 The Generic Genome Browser (GBrowse) is a genome viewer and is GMOD's most popular component. It is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.We use the GBrowse flexible adaptor ...

GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or ...

The GRS was developped to produce various and user-friendly web interfaces on genome annotations. It uses structural and functional annotations stored in Chado database (GMOD schema).
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URGI Transcriptome web interface page.The database is a repository for all transcriptome data such as microarray or macroarray data.
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 GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. ...

Biological data warehouseInterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. Developed by the Micklem lab at the University of Cambridge, InterMine enables the creation of biological databases accessed by sophisticated web query tools. ...

private acces url
JIRA is a project tracking tool for teams building great software.JIRA sits at the center of your development team, connecting the team and the work being done. Track bugs and defects, link issues to related source code, plan agile development, monitor activity, report on ...

The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs (Hoede C. et al. 2014). It browses the whole spectrum of ...

Synteny is gene's order conservation between differents species.Developed by URGI team for J. Salse (INRA Clermont-Ferrand).Publications:
  •  Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes.
Pont, Caroline; Murat, Florent; Guizard, Sebastien; Flores, Raphael; Foucrier, ...

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Prediction: distinguish between mitochondrial and plastid targeting sequences
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The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale. It is distributed under the CeCILL license and deposited to the Agence de Protection des Programmes (APP) under the Inter Deposit Digital Number FR ...

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S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.PresentationSeveral tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have ...

Go to Siregal, the GnpIS Genetic resource module SIReGal, the Plant Genetic Resources Information System of the National Institut for Agronomical Research (INRA), France relies on a ...

free acces url
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The TE_finder suite gathers C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. But we think that the tools are generic enough to be used in other contexts.The suite is mainly composed by four programs BLASTER, MATCHER, GROUPER, ...

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Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.Last version: 1.3
  • Source code in github
  • Changes: Long reads as input are available.
Previous versions
  • Version 1.2.2
    • Source code: ...

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Update: 02 Dec 2011
Creation date: 31 May 2011