Project Number: 5438-32000-025-02
Project Type: Specific C/A

Start Date: Sep 01, 2002
End Date: Sep 30, 2005

Objective:
The objective of this cooperative research project is a curated, open-source, secure Web-accessible data resource for comparative genome analysis in bacteria and viruses. The result is expected to facilitate the identification of genetically engineered pathogens, the classification of pathogen strains based on evolution, the identification of strains and geographical origins, and linking virulence, pathogenicity and host range to sequence differences.

Approach:
Gramene software and other infrastructure will be ported to the Meat Animal Research Center (MARC). Gramene uses a Perl object model based on the bioperl (www.bioperl.org) and Ensembl code bases. The back end is the Oracle relational database, and the front end consists of a set of Perl scripts running in an Apache/mod_perl environment. The advantage of the object model middleware component is that it provides a high-level layer of abstraction between the front end and the back end, insulating front end developers from changes in the database schema and implementation. Gramene will be adapted to accommodate pathogen data and analyses, including DNA fingerprinting, geographical information and pathology. The work is expected to result in a website for a pathogen database; a genome visualization and browsing tool; a BLAST search application program interface (API), an interface to the gene and trait ontology systems, a schema for managing strains, mutants and other types of variants; and web-based curatorial tools.

Project Team

Keele, John Laegreid, William Kappes, Steven Lincoln Stein - Associate Professor 402-762-4251

Project Annual Reports

FY 2003

Related National Programs

Food Animal Production (101)