BioHealthBase: A Web-based Database and Analysis Resource for Francisella

1. Operon Gene Ontology Francisella genomes in BHB New Developments Taxonomy Protein information 1. Select a strain(S) Schu 4 Gene Information Orthologs EC number Localization 2. Select a data type Gene Product Name 3. Select a search term DNA Gyrase Sequence Similarity Search Results Domains Gene Ontology 4. Select data fields to view BioHealthBase Bioinformatics Resource Center (www.biohealthbase.org) provides a comprehensive genomic and proteomic data repository for five groups of pathogens that pose a threat to public health. The bacterial pathogens in BioHealthBase include Mycobacterium tuberculosis, the causative agent of TB, and Francisella tularensis, the causative agent of tularemia. The BioHealthBase includes genome sequences for seven Francisella strains including 3 type A, 3 type B, and F. novicida. New genomes will be added as they are available. Each genome can be searched for protein motifs and by predicted protein localization. Comprehensive protein functional annotations for each locus are available which include EC numbers and gene ontology (GO) annotations, protein structures, protein domains and motifs, orthologous groups, protein cellular localization, metabolic and signaling pathways, immune epitopes, etc. In addition to the integrated genomic data, BioHealthBase also provides user friendly interfaces for data retrieval, data analysis and visualization to assist the biologists in making the best use of the available information. The goal of the BioHealthBase is to provide a resource to the scientific research community to facilitate bioinformatics analyses, and for the development of vaccines, diagnostics and therapeutics for these pathogens. An overview of BioHealthBase database will be presented with a focus on current resources forFrancisella. Supported by NIH N01AI40041 Abstract Home Pages BioHealthBase Gene Details Query Interface Types of Data in BioHealthBase • Basic genome data from Genbank • Genome sequence, gene predictions • Protein Functional annotations • Data enhancements in BioHealthBase • Glimmer gene predictions • EC numbers, GO annotations • Operon predictions • Orthologous groups • Protein cellular localization • Protein domains, motifs • Protein secondary and 3-D structure • Immune epitopes • Mutant phenotype, mutation sites and links to mutant clone library resources • Sequence similarity search (Blast) • Multiple sequence alignment (MUSCLE) • Protein structure viewer (JMol) • Genome Visualization (GBrowse) • Bacterial Genome Annotation Future Development Genome Browser Query Results Display • Francisella SNP data • Protein molecular weight and isoelectric pH predictions • Metabolic pathway data and visualization • Enhanced query interface • Comparative genomics tools (synteny viewer, whole genome alignment viewer) • Immune epitope predictions • Advanced functionalities for protein structure viewer (display epitopes, protein functional sites) • Community annotation Analysis Download Users can 1. Click on ‘Details’ to view the gene/protein information 2. Select genes for downloading information 3. Select genes for further analysis using Workbench BioHealthBase: A Web-based Database and Analysis Resource for Francisella Shubhada Godbole1, Jyothi Noronha1, Burke Squires1, Victoria Hunt1, Ed Klem2, Aihui Wang2, Chris Larsen3, Barbara Mann4 and Richard H. Scheuermann1 1Departmentof Pathology and Division of Biomedical Informatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, 2Northrop Grumman Information Technology, Rockville, MD 20850, 3Vecna Technologies Inc. College Park, MD 20740, 4University of Virginia, Charlottesville, VA 22904. Protein Structure Visualization BioHealthBase Data Summary Tools in BioHealthBase

3. 1. Select a strain(S) CDC1551, H37Ra, H37Rv 4. Select data to view All BioHealthBase Gene Details 2. Select a data type Gene Product Name 3. Select a search term Shikimate Kinase Genome Browser Query Interface Query Results Display Analysis Download Users can 1. Click on ‘Details’ to view the gene/protein information 2. Select genes for downloading information 3. Select genes for further analysis BioHealthBase Gene Details