Pathema Website Functionality Enhancements

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Information about Pathema Website Functionality Enhancements

Published on March 12, 2009

Author: Pathema



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

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

Improved Front Page

Improved Front Page

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

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

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)


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


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

Sybil: Comparative Genomic Region

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

Sybil: Synteny Gradient Display

Pathway Tools

Pathway Tools

Abundance Profiler

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

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 

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