This project's overarching aim is to develop a flexible and extensible infrastructure that will allow the entire community of a given organism to easily contribute to the genome annotation process. We are doing this by integrating and significantly enhancing the functionality existing GMOD tools: Apollo, used for the creation of genomic feature annotations tied to specific locations on the DNA sequence;the Distributed Annotation System (DAS) protocol and associated software, which supports the exchange of annotations over the Internet between researchers;and Generic Genome Browser (GBrowse), used for displaying genome annotations on interactive Web pages. We are combining these applications and building on them to create a novel web-based infrastructure that will offer robust, easy-to-use tools for collaborative, community- driven genome feature annotation by a much broader community of users.

Public Health Relevance

As the number of whole genomes being sequenced increases the annotation of these genomes-what genes are present, the locations of promoter and enhancer sites, and other features-has become the rate- limiting step. Current annotations are unreliable, difficult to compare, and in some cases non-existent. This has serious consequences, because it diminishes the utility of these genome sequences, particularly as they are used for improving the standard of annotation of the human genome which is essential for its maximal exploitation.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM080203-06
Application #
8464732
Study Section
Special Emphasis Panel (ZRG1-BST-Q (01))
Program Officer
Lyster, Peter
Project Start
2007-08-01
Project End
2014-04-30
Budget Start
2013-05-01
Budget End
2014-04-30
Support Year
6
Fiscal Year
2013
Total Cost
$604,264
Indirect Cost
$243,727
Name
Lawrence Berkeley National Laboratory
Department
Genetics
Type
Organized Research Units
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720
Ed, Lee; Nomi, Harris; Mark, Gibson et al. (2009) Apollo: a community resource for genome annotation editing. Bioinformatics 25:1836-7