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Genomics data integration, analysis, and curation using MycoCosm


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The US Department of Energy Joint Genome Institute leads the world in
sequencing of fungal genomes and contributes 40% of genome projects
worldwide. JGI web-based fungal genomics portal MycoCosm integrates
fungal genomics data and analytical tools in one place to provide
access to over 100 fungal genomes sequenced at JGI and elsewhere.
Users may explore fungal genomes in the context of both comparative
genomics and genome-centric analysis. MycoCosm promotes user community
participation in data submission, annotation and analysis, and has
over 4500 unique visitors/month or 35000+ visitors/year.

Published in: Technology
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Genomics data integration, analysis, and curation using MycoCosm

  1. 1. Genomics data integration,analysis, and curation using MycoCosm Robert Riley Igor Shabalov Igor Grigoriev 3 April 2012
  2. 2. US DOE Joint Genome Institute Mission: Genomics user facility in support of DOE missions in: bioenergy biogeochemistry carbon cycling Programs: Fungal, Plant, Microbial, & Metagomics Genome sequencing using latest technologyIllumina HiSeq2000 PacBio Example: JGI fungal sequencing
  3. 3. Fungi in bioenergy degrade lignin & White rot cellulose Phanerochaete chrysosporium BiofuelLignocellulose Brown rot Postia precursors degrade cellulose placenta
  4. 4. Data integration: MycoCosm Comparative View 120+ genomes;5K visitors/month Genome-Centric View
  5. 5. Data Integration: External Links
  6. 6. From GenBank to MycoCosm
  7. 7. Curation: user annotation Users may create improved gene models Your name here! 7
  8. 8. Curated genes 1 100 10 10000 1000 Hebcy1 Hypsu1 Treme1 Agabi_varbis… Paxin1 Phaca1 Plicr1 Jaaar1 Phlgi1 Bjead1_1 Botbo1 Phlbr1 Organism Gansp1 Wolco1 Conpu1 Cersu1 PleosPC9_1 Gymlu1 SerlaS7_9_2 Aurde1 Punst1 Glotr1_1 Fomme1 PleosPC15_2 Pospl1 Fompi1 Trave1 Statistics on manual curation of gene models by increasing number of curations Schco2 Stehi1 Hetan2 Phchr1 Curation: user annotation Lacbi2 Dacsp1 Agabi_varbur… SerlaS7_3_2 Dicsq1 5 0 10 15 20 25 30 Curators8
  9. 9. Curation: user annotationExample: user finds a more sensible gene model Promote to gene catalog Compare to ESTs Transcript page Protein pageCluster viewer 9
  10. 10. Analysis: genome-centric view GC content Sequence conservation Gene catalog ESTs PFAM domains BLAST hitsAlternate gene models 10
  11. 11. Analysis: comparative view 11
  12. 12. Analysis: evolution of lignocellulose degradationCAZy CAZy and lignin-degrading genesgenesOxidoreductasegenes Eastwood et al. Science 2011 Riley et al. in prep
  13. 13. SummaryMycoCosm• Integrates functional and comparative genomic data and analytical tools for energy and environment fungi• Offers tools for community annotation, data repository, and manual curation• Facilitates comparative genome analysis
  14. 14. AcknowledgmentsIgor V. Grigoriev Robert OtillarHenrik Nordberg Alex PoliakovIgor Shabalov Igor RatnereAndrea Aerts Frank KorzeniewskiMike Cantor Xueling ZhaoDavid Goodstein Tatyana SmirnovaAlan Kuo Daniel RokhsarSimon Minovitsky Inna DubchakRoman NikitinRobin A. Ohm