Genomic Resources

Genomic and Transcriptomic data resources are generated in several ‘omics’ projects from ABiMS partners (sequences, gene predictions, alignments, annotations, RNAseq data, microarray…). In the context of this explosion of data, environments facilitating the data analysis (storing, visualizing, editing, exporting…) is essential. The companion websites and GMOD tools helps to meet this need.

The GMOD (Generic Model Organism Database) project is a collection of interconnected open source software tools and databases for visualizing, annotating, and managing genetic and genomic data. GMOD is also an active community of developers and users facing common challenges with their biological data.

Using the GMOD tools, the platform ABiMS aims to develop a coherent and integrated environment to assist collaborators in the analysis and annotation of genomic data. The platform uses the following tools: CHADO (a database), JBrowse (a genome browser to visualize and explore data) and Apollo (a collaborative platform for manual annotation based on JBrowse).

The platform ABiMS initiated this environment within the EMBRC-France project: many genome browsers have been developed in the context of the Marine Model Organism Database. ABiMS hosts today about twenty public and private genomes (marine algae, marine bacteria, marine protists and fungi) for visualization with JBrowse and annotation with Apollo.

Available companions websites

  • HAPAR ANR project ressources web site (private)
  • IMPEKAB ANR project ressources web site (private)
  • JAWS ANR ressources web site (private)
  • Krill ressources web site (private)
  • Sepia officinalis ressources web site (private)
  • Paracentrotus lividus transcriptoms ressources web site (private)
  • Phaeophyceae ressources web site (private)
  • Saccharina latissima transcriptome ressourcesweb site (private)


Available genome browsers and genomic resources

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Algae

  • Chondrus crispus
  • Cladosiphon okamuranus
  • Ectocarpus sp. Ec32
  • Ectocarpus subulatus Bft  
  • Saccharina japonica
  • Brown algae from the PhaeoExplorer project (private)

The metabolic network models are from the Dyliss team (IRISA, Rennes): http://aureme.genouest.org.

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Bacteria

  • 97 marine picocyanobacteria (Cyanobium, Prochlorococcus, Synechococcus)
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Protists

  • Amoebophrya sp. A120 (private)
  • Amoebophrya sp. A25 (private)
  • Ostreococcus taurii
  • Phaeodactylum tricornutum
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Fungi

  • Mucor ambiguus NBRC 6742 (private)
  • Mucor circinelloides B8987 (private)
  • Mucor circinelloides f. lusitanicus CBS277.49
  • Mucor circinelloides f. lusitanicus CBS277.49 (private)
  • Mucor circinelloides CDC-B5328 (private)
  • Mucor circinelloides f. circinelloides 1006PhL (private)
  • Mucor endophyticus CBS 385-95 (private)
  • Mucor fuscus UBOCC-A-109160 (private)
  • Mucor indicus CDC-B7402 (private)
  • Mucor lanceolatus UBOCC-A-109153 (private)
  • Mucor racemosus UBOCC-A-109155 (private)
  • Phycomyces blakesleeanus NRRL1555
  • Rhizopus delemar RA-99880
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