CoPIs: Kevin Childs, Ning Jiang, Shin-Han Shiu, and Yanni Sun (Michigan State University)
Today's DNA sequencing technologies are greatly increasing the availability of genome sequences. These genome sequences have great potential to increase agricultural productivity and provide a foundation for modern, genome-based research. Unfortunately a genome sequence in-and-of itself is of little use unless the locations of the genes within it are identified and their parts properly mapped. The process of locating and mapping the structures of genes within a genome sequence is called genome annotation. Researchers are finding that plant genomes are difficult to annotate for several technical reasons; for example, plant genomes tend to be repeat rich and are often polyploid. The purpose of this project is to adapt and extend MAKER, an established annotation tool, for use on plant genomes. Doing so will help to unlock the potential of sequenced plant genomes to empower genomics- based plant research.
The overarching goal of the project is to produce a plant genome optimized annotation pipeline that can be widely used by the plant research community and will be incorporated as part of the iPlant Cyberinfrastructure. The project will also provide outreach to the plant genomics community by means of tutorials given at various scientific meetings in genome annotation on how to use the MAKER-based plant genome optimized annotation tool. These tutorials will allow smaller plant genome projects to annotate their genomes and to distribute the resulting gene models; in turn, this will enable downstream comparative and functional genomics studies by third parties. Source code will be freely available and distributed in publicly announced releases at www.yandell-lab.org. Stable versions will be available by anonymous FTP and HTTP as software archives (*.tar.gz files). Finally, developer and candidate releases will be managed via subversion repositories. MAKER download pages can be accessed at www.yandell-lab.org/software/index.html.
