Published on March 12, 2009
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
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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