genome sequencing and annotation

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Genome sequencing and annotation Comprehensive identification of virulence gene candidates by various means Bioinformatic prioritization of virulence gene candidates and generation of hypotheses regarding functions of encoded factors Experimental determination of functions of individual virulence factors Integrate knowledge of factors for use in: -eco-evo-systems biology study of pathogen -comparative genomics “Characterization bottleneck” Pathogenomics research overview Steps Limitations (Conserved) hypotheticals and misannotatio next-gen sequencing problems with “mobilom Ongoing curation Protein structure/function prediction Bioinformatic and experimental screens

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Pathogenomics research overview. Steps. Limitations. Genome sequencing and annotation. (Conserved) hypotheticals and misannotation next-gen sequencing problems with “ mobilome ”. Comprehensive identification of virulence gene candidates by various means. - PowerPoint PPT Presentation

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Page 1: Genome sequencing and annotation

Genome sequencing and annotation

Comprehensive identification of virulence gene candidates by various means

Bioinformatic prioritization of virulence gene candidates and generation of hypotheses regarding functions of encoded factors

Experimental determination of functions of individual virulence factors

Integrate knowledge of factors for use in:

-eco-evo-systems biology study of pathogen

-comparative genomics

“Characterization bottleneck”

Pathogenomics research overview

Steps Limitations

(Conserved) hypotheticals and misannotationnext-gen sequencing problems with “mobilome”

Ongoing curation

Protein structure/function prediction

Bioinformatic and experimental screens

Page 2: Genome sequencing and annotation

Andrews-Polymenis et al. 2009

Vivo

Page 3: Genome sequencing and annotation

Sassetti and Rubin 2002

Page 4: Genome sequencing and annotation

Wolfgang et al. 2003

Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa

Page 5: Genome sequencing and annotation

rpoS was downregulated in biofilm

Whiteley et al. 2001

Gene expression in Pseudomonas aeruginosa biofilms

Page 6: Genome sequencing and annotation

Rediers et al. 2005

Page 7: Genome sequencing and annotation

Valdivia and Falkow 1997

Fluorescence-based isolation of bacterial genes expressed within host cells

Page 8: Genome sequencing and annotation

Valdivia and Falkow 1997

Page 9: Genome sequencing and annotation

Chang et al. 2005

A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae

Page 10: Genome sequencing and annotation

Lindeberg et al. 2006

Collmer et al. 2002

Page 11: Genome sequencing and annotation

Tobe et al. 2006

An extensive repertoire of type III secretion effectors in Escherichia coli O157

Page 12: Genome sequencing and annotation

Mazurkiewicz et al. 2006

Signature-tagged mutagenesis

Page 13: Genome sequencing and annotation

Mazurkiewicz et al. 2006

TraSH = Transposon site hybridization

Page 14: Genome sequencing and annotation

Mazurkiewicz et al. 2006

Page 15: Genome sequencing and annotation

Jacobs et al. 2003

Comprehensive transposon mutant library of Pseudomonas aeruginosa

Page 16: Genome sequencing and annotation

Jacobs et al. 2003

Page 17: Genome sequencing and annotation

Jacobs et al. 2003

Comprehensive transposon mutant library of Pseudomonas aeruginosa

Page 18: Genome sequencing and annotation

Medini et al. 2008

Page 19: Genome sequencing and annotation

Medini et al. 2008

Page 20: Genome sequencing and annotation

Metzker 2010

Page 21: Genome sequencing and annotation

Langridge et al. 2009

Page 22: Genome sequencing and annotation

Langridge et al. 2009

Page 23: Genome sequencing and annotation

Sorek and Cossart 2010

Page 24: Genome sequencing and annotation

Sorek and Cossart 2010

Page 25: Genome sequencing and annotation

Sorek and Cossart 2010

Page 26: Genome sequencing and annotation

Chain et al. 2009

Page 27: Genome sequencing and annotation

Chain et al. 2009

Page 28: Genome sequencing and annotation

Howe et al. 2008