Mavrommatis.Genome analysis test case.ppt
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4/15/2009 1 Advancing Science with DNA Sequence A Genome Analysis Case Study with the Integrated Microbial Genome Expert Review (IMG/ER) System Integrated Microbial Genome Expert Review (IMG/ER) System Konstantinos Mavrommatis Genome Biology Program Joint Genome Institute Advancing Science with DNA Sequence Access to your genome + public genomes http://img.jgi.doe.gov/er http://img.jgi.doe.gov/er
Transcript of Mavrommatis.Genome analysis test case.ppt
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Advancing Science with DNA Sequence
A Genome Analysis Case Study with the Integrated Microbial Genome Expert Review (IMG/ER) SystemIntegrated Microbial Genome Expert Review (IMG/ER) System
Konstantinos Mavrommatis
Genome Biology ProgramJoint Genome Institute
Advancing Science with DNA Sequence
Access to your genome+ public genomes
http://img.jgi.doe.gov/erhttp://img.jgi.doe.gov/er
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Advancing Science with DNA Sequence
Advancing Science with DNA Sequence
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Advancing Science with DNA Sequence
Advancing Science with DNA SequenceOrganism page
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Advancing Science with DNA Sequence
Advancing Science with DNA Sequence
IMGcurationcuration
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Advancing Science with DNA Sequence
Gene annotation curation
Advancing Science with DNA SequenceGene page
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Advancing Science with DNA Sequence
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Advancing Science with DNA Sequence
Curation check
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Advancing Science with DNA Sequence
Advancing Science with DNA Sequence
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Advancing Science with DNA Sequence
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Advancing Science with DNA Sequence
Advancing Science with DNA Sequence
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Advancing Science with DNA SequenceCuration check
Advancing Science with DNA Sequence
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Advancing Science with DNA Sequence
IMGdirected searchesdirected searches
Advancing Science with DNA Sequence
Gene searches
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Advancing Science with DNA Sequence
Gene searchby key words
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Advancing Science with DNA Sequence
Advancing Science with DNA Sequence
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Advancing Science with DNA Sequence
IMGdiscovery
Advancing Science with DNA Sequence
user
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Advancing Science with DNA Sequence
Genes with homologs in Gram + (Firmicutes) absent in Gram -
Unknown:sporulation notobserved inobserved inHalothermothrix
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Advancing Science with DNA Sequence
Advancing Science with DNA SequenceSearch for Halothermothrix genes, absent in Gram + (Firmicutes)
known:from cell envelopecharacterization,
RESULT: Halothermothrix genes, absent in Gram +ves (Firmicutes) but present in Gram -ves
consistent with Gram –ultrastructure
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Advancing Science with DNA Sequence
Abundance comparison
•Highest density of carbohydrate ABC transporters except for members of the p pRhizobiaceae, 3% the genome •The phosphotransferase system appears to be in the process of being removed from the genome.
•Enzyme I (Hore_20150) has a frameshift that does not occur at a slippery site,•IIA subunit •IIC subunit •NO IIB subunit
Adaptation to low nutrient environment
Advancing Science with DNA Sequence
Horizontally transferred genes.
