Outils et Logiciels

IGM

Absynte

Archaeal and Bacterial Synteny Explorer.
Web service designed to display local syntenies in completely sequenced prokaryotic chromosomes.
Despalins A, Marsit S, Oberto J. Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters. Bioinformatics. 2011 Aug 11
INRA Le MOULON

ActionMap

Automatisation de la détermination de l'emplacement des loci pour une carte de framework.
Automation of loci assignment to a framework map.
Albini G, Falque M, Joets  J. ActionMap: A web-based software that automates loci asignments to a framework maps. Nucleic Acids Res. (2003) Jul 1;31(13):3815-8
IGM

ARNold

Identification de terminateurs de transcription Rho-indépendants. (IGM)
Easy identification of Rho–independent transcription terminators.
M. Naville, A. Ghuillot-Gaudeffroy, A. Marchais and D. Gautheret. ARNold: A web tool for the prediction of Rho-independent transcription terminators RNA Biology 2011 8:1,1-3.
IGM

BAGET

Service web permettant de faciliter l'extraction de séquences de gènes et de protéines spécifiques provenant de génomes procaryotes annotés entièrement.
Web service designed to facilitate extraction of specific gene and protein sequences from completely determined prokaryotic genomes.
J. Oberto. BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence. Bioinformatics 2008 24(3):424-425.
LRI

BioGuide

BioGuide aide les utilisateur à naviguer dans le labyrinthe des bases de données biologiques.
BioGuide helps users navigate in the maze of biological databases. BioGuide is generic and can be used to query NCBI databases (BioBrowsing) or databases available through the SRS system (BioGuideSRS).
S. Cohen-Boulakia, O. Biton, S. B. Davidson and C. Froidevaux BioGuideSRS: querying multiple sources with a user-centric perspective Bioinformatics (2007) 23 (10): 1301-1303
IGM

CRISPR

Détection facile des CRISPRs (Clustered Regulary Interspacing Short Palindromic Repeats) dans les séquences (allant jusqu'à 67.000.000 pb) soumises par l'utilisateur.
Easy detection of CRISPRs (Clustered Regulary Interspacing Short Palindromic Repeats) in user-submitted sequence data (allows sequences up to 67,000,000 bp).
I. Grissa, G. Vergnaud and C. Pourcel. CRISPRFinder : a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007 May 31.
IGM

Erpin

Logiciel Easy RNA Profile IdentificatioN, programme de recherche de motif d'ARN.
Easy RNA Profile IdentificatioN tool, an RNA motif search program.
Gautheret D, Lambert A. Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles. J Mol Biol. (2001) 313:1003-11
INRA Le Moulon

Eugene-Maize

Prédicteur de gène spécifiquement entrainé pour le maïs.
Maize gene predictor
P. Montalent and J. JoetsEuGène-maize: a web site for maize gene predictionBioinformatics. 2010 May 1;26(9):1254-5.
IGM

FITBAR

Fast Invertigation Tool for Bacterial & Archaeal Regulons
FITBAR permits a fast, accurate and statistically significant prediction of specific protein DNA binding sites on completely sequenced prokaryotic genomes.
Oberto J.FITBAR: a web tool for the robust prediction of prokaryotic regulons. BMC Bioinformatics, 2010, 11(1), 554.
IGM

Frali

Outil de création d'alignements multiples de séquences de familles de protéines hétérogènes incluant des séquences homologues éloignées.
Tool to create accurate multiple sequence alignments of large and heterogeneous proteins families comprising remote homologues.
papier en soumission
LRI

GeneValorization


GeneValorization provides a clear and handful overview of the bibliography corresponding to any gene list of interest.
B. Brancotte, A. Biton, I. Bernard-Pierrot, F. Radvanyi, F. Reyal and S. Cohen-Boulakia.Gene List significance at-a-glance with GeneValorization. Bioinformatics 27(8): 1187-1189 (2011)
IGM/LRI

GenRgenS

Logiciel dédié à la génération aléatoire de séquences génomiques et de structures.
Software tool dedicated to randomly generating genomic sequences and structures.
Y. Ponty, M. Termier and A. Denise. GenRGenS: Software for generating random genomic sequences and structures. Bioinformatics, June 2006 22(12):1534-1535.
INRA Le Moulon

IRILmap

Logiciel de conversion de distance des cartes de liaisons des IRILs, Intermated Recombinant Inbred Lines.
Linkage map distance conversion software for Intermated Recombinant Inbred Lines.
M. Falque. IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains. Bioinformatics 2005 21(16):3441-3442.
IGM/LRI

NestedAlign

Logiciel dédié à la comparaison des structures secondaires d'ARN par paires, soit localement ou globalement.
Software dedicated to RNA secondary structure pairwise comparison, either locally, or globally.
IGM

SynteView

Outil de visualisation de l'ordre des gènes dans les génomes procaryotes et de téléchargement des séquences de gènes appartenant à des blocs conservés de synténie.
Tool to visualize gene order conservation in prokaryotic genomes and to download sequences of genes belonging to conserved synteny blocks.
Lemoine, F.; Labedan, B. & Lespinet, O. SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. BMC Bioinformatics, 2008, 9, 536.
IGM

SyntTax

Eplorateur de synténie et de taxonomie procaryote.
Prokaryotic Synteny & Taxonomy Explorer
Oberto J.SyntTax: a web server linking synteny to prokaryotic taxonomy. BMC Bioinformatics. 2013
IGM/LIRMM

TBminer

Application Web pour faciliter l'analyse des données moléculaires épidémiologiques du complexe de Mycobacterium tuberculosis (MTC).
Web application that aims at facilitating the analysis of Mycobacterium tuberculosis complex (MTC) molecular epidemiology data
IGM/LRI

VARNA

Applet de visualisation des ARN.
Visualization Applet for RNA
K. Darty, A. Denise and Y. Ponty. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, pp. 1974-1975, Vol. 25, no. 15, 2009.