Formulaire pour demande d' homologation cati

CycADS annotation database system to support the development and update of enriched BioCyc databases

http://www.cycadsys.org/
Patrice Baa-Puyoulet^1,4, Augusto F. Vellozo^2,4, Jaime Huerta-Cepas³, Gérard Febvay^1,4, Toni Gabaldon³, Marie-France Sagot^2,4, Hubert Charles^1,4 and Stefano Colella1,4
1 Biologie Fonctionnelle Insectes et Interactions, UMR203 INRA INSA Lyon BF2I, bat INSA Pasteur, 20 ave Albert Einstein, 69621, Villeurbanne Cedex, France

2 Laboratoire de Biométrie et Biologie Évolutive, UMR5558 CNRS Université Lyon 1, bat Grégor Mendel, 43 bd du 11 novembre 1918, 69622, Villeurbanne Cedex, France

3 Centre for Genomic Regulation, Barcelona Biomedical Research Park, Barcelona, Spain

4 BAMBOO, INRIA Rhône-Alpes, France

Keywords: metabolism, arthropods, gene annotation, metabolic pathways.
1. The CycADS Software Project
The Cyc Annotation Database System (CycADS) project started in 2008 during the genome annotation for the pea aphid, Acyrthosiphon pisum. Since the early stages of the quest for all metabolism related genes/proteins in the genome, it was clear that an annotation data management system was needed to allow us (and others) to easily create and further update the BioCyc metabolism network reconstruction of the pea aphid. CycADS allows the collection of heterogeneous annotation information to create dedicated files that are processed with the PathwayTools Software (SRI International) to produce BioCyc interfaces.
2. From AcypiCyc to ArthropodaCyc
CycADS has been successfully used to generate AcypiCyc1, the pea aphid BioCyc database, and we decided to build a metabolic network database for other arthropods, for which the genome sequence is available. We kept the same workflow parameters for collecting data from all used annotation methods (Blast2GO, KAAS, PRIAM). The generated ArthropodaCyc2 database includes, at present, metabolic reconstructions for 11 arthropods: Acyrthosiphon pisum, Aedes aegypti, Anopheles gambiae, Apis mellifera, Culex quinquefasciatus, Daphnia pulex, Ixodes scapularis, Nasonia vitripennis, Pediculus humanus corporis, Tribolium castaneum and Drosophila melanogaster (for this last species, both the CycADS version and the FlyCyc database manually curated by the FlyBase team are available). Collecting and organizing information into databases is useful for the researchers studying the metabolism of their newly sequenced model organisms (more arthropod genomes will be sequenced in the near future through the i5K Arthropod Sequencing initiative), and it allows them to better understand different aspects of arthropod biology through comparative studies.

Thanks to the CycADS software, we included, in each database, information on annotation sources and links to genomics databases (including AphidBase, BeetleBase, VectorBase, Hymenoptera Genome Database, FlyBase and wFleaBase). Future plans include adding other sequenced genomes to ArthropodaCyc and the generation of another BioCyc-like database centred on the arthropod endosymbiosis for which both host and symbiont genomes have been sequenced (a beta version of ArtSymbioCyc is already available).

FrameDP: sensitive peptide detection on noisy matured sequences

http://iant.toulouse.inra.fr/FrameDP/

Jérôme Gouzy¹, Sébastien Carrere¹ and Thomas Schiex^2,*

¹ Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, F-31320 Castanet Tolosan, France

² Unité de Biométrie et d’Intelligence Artificielle UR 875, INRA, F-31320 Castanet Tolosan, France
Transcriptome sequencing represents a fundamental source of information for genome wide studies and transcriptome analysis and will become increasingly important for expression analysis as new sequencing technologies takes over array technology. The identification of the protein coding region in transcript sequences is a prerequisite for systematic amino acid level analysis and more specifically for domain identification. In this paper, we present FrameDP, a self training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.
Compared to the alternative prot4EST pipeline, FrameDP has strong qualitative advantages. The most important of all is its ability to self-train directly on EST clusters instead of requiring curated cDNA sets to train the underlying ESTScan and DECODER (Fukunishi and Hayashizaki, 2001) software. Thanks to FrameD, FrameDP also directly integrates the similarity information inside the CDS prediction process instead of performing separate predictions. Beyond this, FrameDP can use multiple Markov models and can handle degenerated sequences both for signals (STOP/START codons) and inside Markov models.
The PERL-CGI server provides life scientists with a user-friendly interface to the pipeline (limited to batches of fifty sequences). It also provides an automatic protein description based on InterPro domain content. The functional annotation capabilities rely on BioMoby web services and on the REMORA workflow manager (Carrere and Gouzy, 2006).
A package for large scale local application is provided under the CECILL2 open source licence. It includes FrameD, NCBI-BlastX and paraloop. The pipeline is controlled by a single program, configurable using one configuration file.
14 citations dans google scholar; 9 citations dans le WOS.

iANT : integrated ANnotation Tool

1. 
   http://iant.toulouse.inra.fr/S.meliloti; http://iant.toulouse.inra.fr/R.solanacearum; http://iant.toulouse.inra.fr/X.species
   

Objectifs :

Depuis 1998, la plateforme bioinformatique du Laboratoire des Interactions Plantes Micro-organismes développe des outils pour l'annotation semi-automatique structurale et fonctionnelle des génomes. iANT est à la fois une boîte à outils proposant des outils pour réaliser l'annotation et l'analyse des données de génomiques, ainsi qu'une plateforme permettant aux biologistes d'accéder à ces données, les modifier et les publier sous forme de portail web.

La boîte à outil propose une batterie de scripts documentés destinés à l'annotation fonctionnelle. Ces outils sont utilisés par les bioinformaticiens via leur intégration dans d'autres outils. La majorité est également disponible via la technologie des Web-services BioMOBY ou via la plateforme Mobyle.
La plateforme web destinée aux biologistes authentifiés permet à ces derniers de :

• 
  modifier l'annotation structurale et fonctionnelle automatique des différents objets biologiques.
  
• 
  rechercher des informations sur leur génome via un moteur de recherche et/ou via des outils d'analyse de séquence classiques (serveur Blast, serveur PatScan)
  
• 
  naviguer dans le génome via des représentations graphiques de ce dernier
  
• 
  lancer des analyses complexes via des workflows Remora
  

Développements:

Les développements sont réalisés sur la Plateforme Bioinformatique du LIPM. Ils consistent principalement en la maintenance évolutive des outils (ex : migration SRS vers Lucene, modèle des données orienté objet), l'intégration de nouveaux outils et l'automatisation du déploiement de portails web dans le cadre de projets de reséquençage d'organismes prokaryotes à grande échelle.

Références des publications des génomes ayant utilisé iANT :

Galibert F, et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science. 2001 Jul 27;293(5530):668-72.

Salanoubat M, et al. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature. 2002 Jan 31;415(6871):497-502.

Sullivan JT, et al. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol. 2002 Jun;184(11):3086-95.

Saillard C, et al. The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome. BMC Genomics. 2008 Apr 28;9:195.

Pieretti I, et al. The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics. 2009 Dec 17;10:616.