Recently, sequencing costs have dropped sharply due to increased throughput, simplification, and affordability of second (or even third and fourth) generation sequencing technologies, leading to an explosion of smaller sequencing facilities. However, despite the increased rate of sequence generation, there has not been a commensurate increase in access to computational resources to support high-quality sequence processing and analysis. The Annotation Engine has been effective in providing prokaryotic annotation services to the community for four years;however the analysis needs of researchers now far exceed prokaryotic genome annotation. In this work we plan to substantially expand the analysis pipelines offered in our service to include sequence assembly, comparative genomics, and transcriptome analysis. This will result in the evolution of the Annotation Engine into the Analysis Engine. Furthermore, we will also increase the interoperability of our tools with other popular bioinformatics tools. Finally, we will engage in active outreach and training. This combination of activities is expected to enable researchers to rapidly perform analyses that are vital for public health and have significant impact in the areas of drug targeting, diagnostic marker and genotyping, infectious disease control, rapid response to pathogen outbreaks and vaccine development.

Public Health Relevance

For four years, the Annotation Engine has provided structural and functional annotation and analysis resources for scientists working on prokaryotic organisms important to human health. So far, the Institute for Genome Sciences Annotation Engine has processed over 500 genomes or other sequences of interest. Of these, nearly 200 are human pathogens and another 100 are plant and animal pathogens or other host- associated species. In this proposal we aim to add several more analysis pipelines to the service that will result in the evolution of the Annotation Engine into the Analysis Engine. The additional pipelines we propose to add to the service will provide comprehensive advanced analysis resources to the research community. Furthermore, additional tool integration, as planned in this proposal, will expand the suite of visualization and analysis resources that researchers will be able to bring to bear on their data. This combination of activities is expected to enable researchers to rapidly perform analyses that are vital for public health and have significant impact in the areas of drug targeting, diagnostic marker and genotyping, infectious disease control, rapid response to pathogen outbreaks and vaccine development.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
5R01GM080227-07
Application #
8643248
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Brazhnik, Paul
Project Start
Project End
Budget Start
Budget End
Support Year
7
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Maryland Baltimore
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
City
Baltimore
State
MD
Country
United States
Zip Code
21201