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

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.

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. subtilis B. pumilus All Clostridium (25) C. perfringens (9) C. botulinum (9) C. difficile C. thermocellum C. acetobutylicum C. tetani C. butyricum C. novyi C. phytofermentans All Burkholderia (28) B. mallei (11) B. pseudomallei (10) B. thailandensis B. cenocepacia B. sp. B. phages (4) P. aeruginosa R. solanacearum All Entamoeba (3) E. histolytica E. dispar E. invadens

Pathema Header

Pathema Header A quick link to locus and annotation search is available at the top of all Pathema pages

Pathema Header An organism menu allows you to see all genomes available on Pathema

Pathema Header The Header Menu

Pathema Menus The Header Menu offers an efficient tool based way to navigate through Pathema

Pathema Menus Clicking on “Searches” takes you to a detailed list of the tools available

Gene Search: Annotation The information “i” gives you details about the tool Breadcrumbs to orient you

Gene Search: Annotation

Gene Search: Evidence

Gene Search

Gene Search: Evidence

Carts

Gene Cart

Carts

Genome 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.

Participation and access to community curation tool.

Submission of experimentally characterized proteins.

Participation in future usability studies.

Community recognition.

Available Pathema Genomes

Detailed Strain Information 52-year old male rice farmer 1710a 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 farmer 1106a 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

52-year old male rice farmer

1710a

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 farmer

1106a

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.

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 Search

Pathogenicity

Therapeutics

MUMmer: Align Genomes

Genome Homology Graph

Genome Homology Graph

Protein Scatter Plot

Color by Identity

Change the Settings

GC Comparison Graph

Pseudo-2D Gel

Downloads

Batch Download

Batch Download

Downloads

Gene Attribute Download

Gene 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

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

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

Acknowledgements P.I.: Granger Sutton Funding: NIAID Subcontract: University of Maryland, Baltimore, IGS Informatics Engineers Informatics Analysts Tanja Davidsen (manager) Scott Durkin (manager) Erin Beck Ramana Madupu Alex Richter Susmita Shrivastava Kevin Galinsky Bob Dodson Jay Sundarm Derek Harkins Seth Schobel Lis Caler Owen White (University of Maryland, Baltimore) Anu Ganapathy YongMei Zhao Josh Orvis Aaron Gussman Kevin Galens Jonathon Crabtree

P.I.: Granger Sutton

Funding: NIAID

Subcontract: University of Maryland, Baltimore, IGS

Informatics Engineers Informatics Analysts

Tanja Davidsen (manager) Scott Durkin (manager)

Erin Beck Ramana Madupu

Alex Richter Susmita Shrivastava

Kevin Galinsky Bob Dodson

Jay Sundarm Derek Harkins

Seth Schobel Lis Caler

Owen White (University of Maryland, Baltimore)

Anu Ganapathy YongMei Zhao

Josh Orvis Aaron Gussman

Kevin Galens Jonathon Crabtree