pathema: a clade specific bioinformatics resource center

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


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


An organism An organism menu allows you menu allows you

to see all to see all genomes genomes

available on available on PathemaPathema


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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

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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

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

DownloadsDownloads

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

pathema: a clade specific bioinformatics resource center

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