Oral Pathogen Sequence Databases at Los Alamos National Laboratory

Objectives: The Oral Pathogen Genome Sequence Database (ORALGEN), funded by the National Institute of Craniofacial and Dental Research (NIDCR) of NIH, is a specialized sequence database managed at the Los Alamos National Laboratory in support of oral pathogen research. The ultimate goal of this project is to provide a comprehensive resource with regard to molecular data of oral pathogens and to present value-added sequence records for which compilation and analysis go hand-in-hand.

Methods: We have implemented existing bioinformatics tools and relational databases to perform detailed analysis of proteins and genomes of oral pathogens. In addition, we also manually curate the annotation of some important organisms presented on our website.

Results: The database currently encompasses primary and derived molecular sequence data for Actinobacillus actinomycetemcomitans, Actinomyces naeslundii, Fusobacterium nucleatum ATCC 25586, Fusobacterium nucleatum polymorphum, Porphyromonas gingivalis, Prevotella intermedia, Streptococcus gordonii, Streptococcus mitis, Streptococcus mutans, Streptococcus sanguinis, Tannerella forsythensis, Treponema denticola, several herpesviruses and 23 oral pathogen plasmids. In addition to tracking molecular sequences and the relevant literature, we perform basic analyses to facilitate research, interact with the research community through attendance at major meetings, assist individual researchers, and publish a website consisting of relational databases, tables of basic information, and mini-reviews. We also serve as a training center in bioinformatics. Over the past summer, Oralgen has been conducting a series of analysis including base composition Analysis for five oral bacteria, hypothetical proteins ranking for P. gingivalis and S. mutans, B-cell epitope prediction for P. gingivalis, IS elements and proteome cellular location prediction. All these results were released at Oralgen website http://oralgen.lanl.gov/.

Conclusion: We continue to expand our collection of oral pathogens for detailed analysis and to provide dental research community with valuable information.

This work is supported by NIH NIDCR under LANL contract no. Y1-DE-6006-02