pathema: a clade specific bioinformatics resource center
DESCRIPTION
Conference: Meeting at NIH, Sep. 22, 2008 Presenter: Lauren BrinkacTRANSCRIPT
PATHEMA: A CLADE SPECIFIC BIOINFORMATICS RESOURCE
CENTER
Lauren Brinkac
The J. Craig Venter Institute
What is Pathema?
Pathema (http://pathema.jcvi.org)
A NIAID Bioinformatics Resource Center designed to support bio-defense and infectious disease research.
Pathema provides detailed curation of six target pathogens:
Category A priority pathogens: Bacillus anthracis, Clostridium botulinum
Category B priority pathogens: Burkholderia mallei, Burkholderia pseudomallei,
Clostridium perfringens, Entamoeba histolytica
What is Pathema?
• A customized suite of sophisticated bioinformatics software
• An extensive library of literature and manually curated data
• Comparative analysis tools customized to retrieve, display, and compute results relevant to ongoing bio-defense research
Overarching Goal: to provide core resources that will accelerate scientific progress on understanding, detecting, diagnosing and treating Category A-C pathogens and other pathogens involved in new and re-emerging infectious diseases.
All Bacillus (24)
B. anthracis (17)
B. cereus (3)
B. thuringiensis (2)
B. subtilisB. pumilus
All Clostridium (25)
C. perfringens (9)
C. botulinum (9)
C. difficileC. thermocellumC. acetobutylicumC. tetaniC. butyricumC. novyiC. phytofermentans
All Burkholderia (28)
B. mallei (11)
B. pseudomallei (10)
B. thailandensisB. cenocepaciaB. sp.B. phages (4)
P. aeruginosaR. solanacearum
All Entamoeba (3)
E. histolyticaE. disparE. invadens
PathemaPathema Header Header
PathemaPathema Header Header
A quick link to A quick link to locus and locus and annotation annotation search is search is
available at the available at the top of all top of all
Pathema pagesPathema pages
PathemaPathema Header Header
An organism An organism menu allows you menu allows you
to see all to see all genomes genomes
available on available on PathemaPathema
PathemaPathema Header Header
The Header The Header MenuMenu
PathemaPathema Menus Menus
The Header Menu The Header Menu offers anoffers an
efficient tool efficient tool based way to based way to
navigate through navigate through PathemaPathema
PathemaPathema Menus Menus
Clicking on Clicking on “Searches” takes “Searches” takes you to a detailed you to a detailed list of the tools list of the tools
availableavailable
Gene Search: AnnotationGene Search: Annotation
The information “i” The information “i” gives you details gives you details about the toolabout the tool
Breadcrumbs to orient Breadcrumbs to orient youyou
Gene Search: AnnotationGene Search: Annotation
Gene Search: EvidenceGene Search: Evidence
Gene SearchGene Search
Gene Search: EvidenceGene Search: Evidence
CartsCarts
Gene CartGene Cart
CartsCarts
Genome CartGenome Cart
Pathema Home Page
Community Registration
Participation and access to community curation tool. Submission of experimentally characterized proteins. Participation in future usability studies. Community recognition.
Available Pathema Genomes
Detailed Strain Information52-year old male rice farmer1710a
• Isolated from blood culture 1996• Disseminated disease• Survived to discharge• Relapsed in 1999
1710b• Isolated from blood culture 1999• Died on day of admission
23-year old female rice farmer1106a
• Isolated from pus aspirated from liver abcess 1993• Survived to discharge• Relapsed in 1996
1106b• Isolated from pus aspirated from liver abcess 1999• Survived to discharge
All vs. Protein Alignment
All of the proteins in Pathema are routinely blasted against one another and the blast results are stored in the database.
When a new genome is added to the database the all vs. all searches are re-run.
The information from the All vs. All blast searches is displayed throughout Pathema for cross genome analyses.
Pathema Blast
Protein Motif SearchProtein Motif Search
Pathogenicity
Therapeutics
MUMmer: Align GenomesMUMmer: Align Genomes
Genome Homology GraphGenome Homology Graph
Genome Homology GraphGenome Homology Graph
Protein Scatter PlotProtein Scatter Plot
Color by IdentityColor by Identity
Change the SettingsChange the Settings
GC Comparison GraphGC Comparison Graph
Pseudo-2D GelPseudo-2D Gel
DownloadsDownloads
Batch DownloadBatch Download
Batch DownloadBatch Download
DownloadsDownloads
Gene Attribute DownloadGene Attribute Download
Gene Attribute DownloadGene Attribute Download
What is the future of Pathema?
We are relying on your feedback! Data exchange & Integration Genome sequence analysis Custom data analysis Custom tool development
Clade-specific Annotation Jamborees: Incorporate Expert Annotation Free JCVI clade-specific workshops
New Genome Sequences & Annotation Data
JCVI’s Annotation Service
A free service which provides automated annotation and tools for analysis of another center's prokaryotic sequence.
Two components:
• Production of output from JCVI's automated annotation pipeline - includes search results and automatically generated annotation in a MySQL database and associated files.
• The manual annotation tool Manatee - an open source web based interface for interacting with and editing annotation data.
JCVI Annotation Training Course
AcknowledgementsP.I.: Granger SuttonFunding: NIAIDSubcontract: University of Maryland, Baltimore, IGS
Informatics Engineers Informatics AnalystsTanja Davidsen (manager) Scott Durkin (manager)Erin Beck Ramana Madupu
Alex Richter Susmita ShrivastavaKevin Galinsky Bob DodsonJay Sundarm Derek HarkinsSeth Schobel Lis Caler
Owen White (University of Maryland, Baltimore)Anu Ganapathy YongMei Zhao Josh Orvis Aaron GussmanKevin Galens Jonathon Crabtree