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.

Prédiction de gènes


VersionMAJ

GenePRIMP

0.32013-04-19DownloadDoc
Identification of anomalous gene calls The GenePRIMP pipeline consists of a series of computational units that identify erroneous gene calls and missed genes, and then correct a subset of the identified anomalous features. The data input to GenePRIMP needs to be a file of gene calls in GenBank or EMBL format. As its output, GenePRIMP generates reports of identified anomalies, plus a corrected EMBL file.

Remarque
Run Unix # geneprimpRun Web #

VersionMAJ

genscan

1.02007-10-24DownloadDoc

Remarque
Run Unix # genscanRun Web #

VersionMAJ

glimmer

glimmer-3.022008-12-12DownloadDoc
Glimmer (Gene Locator and Interpolated Markov ModelER) prédit la position des gènes dans une séquence d'ADN (bactérie, archae, virus) en s'appuyant sur des modèles de Markov.

Remarque
Run Unix # glimmer3Run Web #

VersionMAJ

gmorse

1.02009-08-05DownloadDoc
G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.

Remarque
Run Unix # gmorse -hRun Web #

VersionMAJ

metagene

2007-05-04DownloadDoc
Gene Finding Program for Metagenomics MetaGene predicts prokaryotic genes on anonymous genomic sequences. Fragmented sequences (longer than 100 bp) can be accepted.

Remarque
Run Unix # metagene [multi-fasta] Run Web #

VersionMAJ

MetaGeneAnnotator

- 2009-01-26DownloadDoc
Version améliorée du programe d'annotation de données métagénomiques Metagene. Prediction de genes procaryotes à partir d'un génome ou d'un set de génomes anonymes. Particulierement adapté aux analyses métagénomiques.

Remarque
Run Unix # metageneannotatorRun Web #

VersionMAJ

prodigal

2.602013-03-26DownloadDoc
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include: Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less. Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly). Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%. GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations. Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown. Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.

Remarque Prodigal Reference: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11(1):119. (Highly Accessed)
Run Unix # prodigal -h Run Web #

VersionMAJ

ratt

-2010-10-29DownloadDoc
RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

Remarque
Run Unix # start.ratt.sh Run Web #

VersionMAJ

SHOW

201111092011-11-11DownloadDoc
SHOW (Structured HOMgeneity Watcher) permet une utilisation souple des modeles de chaines de Markov cachees. L'utilisateur peut construire son propre modele dont les parametres peuvent ensuite etre estimes par maximum de vraisemblance avec l'algorithme EM. Le modele peut alors servir a faire des predictions avec l'algorithme forward-backward (posterior decoding) ou avec l'algorithme de Viterbi. Il peut aussi servir a simuler des sequences. SHOW implemente aussi un detecteur de genes bacteriens. L'utilisateur n'a alors pas a se soucier du modele ni des parametres. SHOW a deja servi a annoter des genomes complets publies.

Remarque
Run Unix # show_viterbi # show2mugen.plRun Web #

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