genomics data integration, analysis, and curation using mycocosm
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Genomics data integration,
analysis, and curation using
MycoCosm
Robert Riley
Igor Shabalov
Igor Grigoriev
3 April 2012
US DOE Joint Genome Institute
Mission: Genomics user facility in
support of DOE missions in:
bioenergycarbon cycling
biogeochemistry
PacBioIllumina HiSeq2000
Genome sequencing
using latest technology
Programs: Fungal, Plant,
Microbial, & Metagomics
Example: JGI fungal sequencing
Fungi in bioenergy
LignocelluloseBiofuel
precursors
White rot
Phanerochaete
chrysosporium
degrade
lignin &
cellulose
Brown rot
Postia
placentadegrade
cellulose
Data integration: MycoCosm
MycoCosm
jgi.doe.gov/fungi
120+ genomes;
5K visitors/month Genome-Centric View
Comparative View
Data Integration: External Links
From GenBank to MycoCosm
7
Curation: user annotation
Your name here!
Users may
create improved
gene models
8
Curation: user annotation
0
5
10
15
20
25
30
1
10
100
1000
10000
Heb
cy1
Hypsu1
Trem
e1
Agabi_varbis…
Paxin1
Phaca1
Plicr1
Jaaar1
Phlgi1
Bjead1_1
Botbo1
Phlbr1
Gansp1
Wolco1
Conpu1
Cersu1
PleosPC9_1
Gym
lu1
SerlaS7_9_2
Aurde1
Punst1
Glotr1_1
Fomme1
PleosPC15_2
Pospl1
Fompi1
Trave1
Schco2
Steh
i1
Hetan2
Phchr1
Lacbi2
Dacsp1
Agabi_varbur…
SerlaS7_3_2
Dicsq1
Statistics on manual curation of gene models
Organism
Cura
ted g
enes
Cura
tors
by increasing number of curations
9
Curation: user annotation
Example: user finds a more sensible gene model
Compare
to ESTs
Promote to
gene catalog
Transcript pageProtein page
Cluster viewer
10
Analysis: genome-centric view
Sequence
conservation
GC content
Gene
catalog
ESTs
BLAST hits
PFAM domains
Alternate gene
models
11
Analysis: comparative view
Analysis: evolution of
lignocellulose degradationCAZy
genes
Oxidoreductase
genes
CAZy and lignin-degrading genes
Eastwood et al. Science 2011 Riley et al. in prep
Summary
MycoCosm
• 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
Acknowledgments
Igor V. Grigoriev
Henrik Nordberg
Igor Shabalov
Andrea Aerts
Mike Cantor
David Goodstein
Alan Kuo
Simon Minovitsky
Roman Nikitin
Robin A. Ohm
Robert Otillar
Alex Poliakov
Igor Ratnere
Frank Korzeniewski
Xueling Zhao
Tatyana Smirnova
Daniel Rokhsar
Inna Dubchak
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