Arrêt de l'ensemble des services de la plateforme Migale à partir du lundi 3 avril 2017

La plateforme Migale sera indisponible du 3 au 10 avril 2017. Cette indisponibilité est dûe à l'arrêt du DataCenter Ile-de-France qui héberge l'infrastructure de la plateforme.

Merci d'avance de votre compréhension.

Pour toutes questions ou informations supplémentaires, merci de contacter help.migale@jouy.inra.fr.

Génome complet


VersionMAJ

apollo

1.11.82013-08-11DownloadDoc
Apollo is a genomic annotation viewer and editor. There are currently two branches of Apollo, one primarily used for genome browsing and maintained at Ensembl, and the other primarily used for genome annotation and maintained at the Berkeley Drosophila Genome Center. The latter is part of the GMOD project.

Remarque
Run Unix # apolloRun Web #

VersionMAJ

artemis

15.02013-08-07DownloadDoc
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.

Remarque
Run Unix # artRun Web #

VersionMAJ

augustus

2.7 2013-12-12DownloadDoc
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally. It is open source so you can compile it for your computing platform. You can now run AUGUSTUS on the German MediGRID. This enables you to submit larger sequence files and allows to use protein homology information in the prediction. The MediGRID requires an instant easy registration by email for first-time users.

Remarque
Run Unix # augustus [parameters] --species=SPECIES queryfilenameRun Web #

VersionMAJ

cgview

-2011-05-27DownloadDoc
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types, see the CGView gallery.

Remarque
Run Unix # cgviewRun Web #

VersionMAJ

CLC Sequence Viewer

6.42010-09-12DownloadDoc
A Sequence Viewer for basic bioinformatics. CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.

Remarque
Run Unix # clcseqview6Run Web #

VersionMAJ

MuGeN

200609192007-01-05DownloadDoc
MuGeN (Multi-Genome Navigator) est un outil interactif permettant une exploration dans plusieurs géomes annotés complets par des résultats d'analyse in silico. Il dispose également d'un mode d'exécution en mode batch lui permettant de servir de générateur d'images à divers formats. Ce mode de fonctionnement le prédispose à être intégré à des sites Web pour l'affichage de cartes physiques annotées. MuGeN is a software package for the visual exploration of multiple annotated genome portions. It is capable of simultaneously displaying genome portions loaded from various sources both local and remote and mix these with analysis result plots. It can also be used to generate images of these displays in a wide range of formats (PNG, PostScript, IMAP, XFig).

Remarque La commande : mugenv est suffisante pour lancer l'environnement graphique, mais elle ne charge aucun génome et les fenêtres paraîtront donc un peu vides. Plus fréquemment, on fera : mugenv /chemin/vers/un/fichier/genbank.gbk pour explorer le fichier en question. Les numéros de version de MuGeN correspondent à leur date de sortie, et sont affichées dans la barre titre de sa fenêtre graphique. La dernière en date est la 20040726 qui est celle installée sur topaze et adm.
Run Unix # mugenv ou mugenv /chemin/vers/un/fichier/genbank.gbkRun Web #

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