BioHealthBase: A Web-based Database and Analysis Resource for Francisella Shubhada Godbole 1, Jyothi Noronha 1, Burke Squires 1, Victoria Hunt 1, Ed Klem 2, Aihui Wang 2, Chris Larsen 3, Barbara Mann 4 and Richard H. Scheuermann 1 1 Department of Pathology and Division of Biomedical Informatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, 2 Northrop Grumman Information Technology, Rockville, MD 20850, 3 Vecna Technologies Inc. College Park, MD 20740, 4 University of Virginia, Charlottesville, VA BioHealthBase Bioinformatics Resource Center ( 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 for Francisella. Supported by NIH N01AI40041 Abstract 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 Types of Data in BioHealthBase Tools in BioHealthBase Protein Structure Visualization BioHealthBase Data Summary Home Pages Francisella genomes in BHB New Developments Query Interface 1. Select a strain(S) Schu 4 2. Select a data type Gene Product Name 3. Select a search term DNA Gyrase 4. Select data fields to view Query Results Display 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 Analysis Download Genome Browser BioHealthBase Gene Details Taxonomy Gene Information Operon Protein information EC numberLocalization Domains Gene Ontology Orthologs Gene Ontology Sequence Similarity Search Results Future Development 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

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