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United States Department of Agriculture

Agricultural Research Service

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Research Project: Legume Information System - a Legume Bioinformatics Resource

Location: Corn Insects and Crop Genetics Research

Project Number: 5030-21000-062-03
Project Type: Specific Cooperative Agreement

Start Date: Jun 29, 2012
End Date: Jun 30, 2014

Objective:
Curate, develop and serve visualization and analysis tools for a legume genomic database and portal, with emphasis on agronomically relevant genomic data. The Legume Information System (LIS) acts as both a long-term repository for legume genetic/genomic data (including data generated by NRI projects) and a portal to data maintained primarily at other sites. LIS also provides tools to retrieve, analyze, compare and visualize legume genetic/genomic data. The LIS database and website (http://comparative-legumes.org) needs to accommodate multiple new complete genome sequences, and large quantities of new data, particularly from high throughput sequencing technologies.

Approach:
The cooperator will work with the ADODR to continue incorporating relevant data from NRI-funded and other public legume projects, and to continue developing and serving the Legume Information System web site and associated databases. The cooperator will also: Provide research support services to legume researchers, as appropriate to the scope of available project funding. Revise web interfaces to provide more intuitive access to data and bioinformatic tools. Interact with users to seek feedback on user needs and on interface useability. Work with the ADODR and the SoyBase group to design and implement reports of genetic trait data, to update genetic maps held in LIS, to relate trait data to the genetic maps, and to accommodate genome browser and gene family data sets and bioinformatic tools developed in the SoyBase group. Continue improvement of the organization, management, and flow associated with LIS tools, including tools at the comparative-legumes.org website. As time and resources allow, develop software to aid in assessment of gene transcript assemblies, particularly those built from RNA-Seq data. Establish standards and methodologies for variant (SNP) annotation of transcriptome assemblies, particularly those intended to be made available as reference assemblies to the legume community. Participate in outreach activities to the legume research community, including at relevant conferences. Contribute to the bioinformatics software community by providing open-source software through GitHub or other suitable portals. Participate in a Working Group meeting to solicit feedback from key stakeholders and advisors. Work closely with technical and user oversight groups convened by USDA-ARS, to ensure that the project deliverables meet current and anticipated needs such as increased priorities of legume allergens and Asian Soybean Rust. Conduct focused transcriptome sequencing as specified by the ADODR, consistent with funds designated for this purpose. Implement and deliver bioinformatics information and software in accordance with the specifications of the SCA.

Last Modified: 10/21/2014
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