Conference: Annual BRC Meeting (BRC6), Oct 28-29, 2008 in Ft. Lauderedale, Florida. Presenter: Tanja Davidsen

1. Pathema Website Functionality
Enhancements:
Pathema gets its Sexy Back
Tanja Davidsen, Ph.D.
J. Craig Venter Institute

2. Improved Front Page

3. Improved Front Page

4. Improved Searches using Lucene
• Improved speed and functionality of the search queries
on Pathema
• An open source information retrieval library supported by
Apache
• At the core of the Lucene logical architecture is a
document containing fields of text, independent of file
format
• Prevents us from hitting the database for searches,
especially helpful for inexact searches
• Used by Wikipedia, Monster, SourceForge, UniProt and
EBI

5. Improved Searches using Lucene
• Improves our search speed from 30+s to 1-3s
• Filters will allow us to let the users build even
more complex queries:
Search for all genes in organism B.anthracis starting

with the “dna” and assigned GO ID GO:0003677

6. GBrowse (GMOD)
• The most popular GMOD viewer
• Used to replace and/or accompany our in
house genome viewers
• Order and appearance of tracks are
customizable by administrator and end-user
• Supports third party annotation using GFF
formats
• Third-party feature loading
• Customizable plug-in architecture (e.g. run
BLAST, find oligonucleotides, design
primers)

7. Gbrowse

8. ClosTox: The Clostridum Toxin DB
• The Clostridium community is primarily
interested in the toxin genes
• We created a specialty toxin and neurotoxin
associated proteins (NAPs) database for
browsing on the Clostridium site
• Data for the database provided by Clostridium
researchers/community
• Very successful debut at the last Botulism
meeting

9. ClosTox

11. Sybil: Comparative Genomic Region
• Compares a reference to selected
comparison genomes by protein clusters
• Specify how many clustered genes a non-
reference sequence region must have in
common to with the reference

12. Sybil: Comparative Genomic Region

13. Sybil: Synteny gradient display
• A color-coded display of conserved synteny
between two or more sequences
• Select a reference sequence (bottom of the
display) with the genes color-coded from the 5’
end to the 3’ end
• Orthologs in the comparison genomes are
shown in the color of the ortholog from the
reference genome
• As a result one can see large and small-scale
rearrangements at a glance, in addition to
regions that may be inserted in one sequence
relative to another

14. Sybil: Synteny Gradient Display

15. Pathway Tools

16. Pathway Tools

18. Abundance Profiler

19. New Data Types
• Virulence Factors
• Epitopes
• Experimentally characterized
genes/proteins
• Multidrug transporters
• Genomic islands
• Community requested databases
(ClosTox)

20. Acknowledgements
• PI: Granger Sutton (JCVI)
• Subcontract: Owen White (University of Maryland, Baltimore, IGS)
• Project Manager: Lauren Brinkac
JCVI Informatics Engineers Analysts

Tanja Davidsen (manager) Scott Durkin (manager)

Erin Beck Ramana Madupu

Alex Richter Susmita Shrivastava

Kevin Galinsky Bob Dodson

Jay Sundaram Derek Harkins

Seth Schobel Lis Caler

IGS Informatics Engineers

Anu Ganapathy YongMei Zhao

Josh Orvis Aaron Gussman

Kevin Galens Jonathon Crabtree
