2007 Annual Report 1a.Objectives (from AD-416) The objective of this project is to migrate selected portions of SoyBase into a relational database structure and to conduct comparative analyses between the soybean genome and the genomes of other plants. 1b.Approach (from AD-416) (1) Working with the USDA/ARS, the cooperator will review the near-term bioinformatics needs for the reposition, curation, and analysis of soybean genetic and genomic data, including a critical review of the status of the existing information resources for soybean (in particular, SoyBase). (2) The Cooperator, in close collaboration with the ADODR will seek to anticipate future user requirements, particularly with respect to genetic mapping data, germplasm, and high-throughput genomic data that are being generated by NSF-funded legume genome projects.. 3)The current state of SoyBase data will be reviewed and computer code and models developed to move SoyBase data into a relational database structure. (4) Soybean genomic data and data from other dicots will be used to study the organization and evolutionary history of the soybean genome. (5) Technical and user advisory groups will be convened by USDA/ARS to insure that the project deliverables meet current and anticipated user needs. This work will be synergistic with the ongoing ARS collaboration with NCGR in the development of a Legume Information System. 3.Progress Report This report documents research conducted under a Specific Cooperative Agreement between ARS and Iowa State University. Additional details of research are in the report for the parent project 3625-21000-038-00D Curation and Development of SoyBase and its Integration with other Plant Genome Databases. This project is part of NP 301 Plant Genetic Resources, Genomics and Genetics Improvement, and fits within Action Plan Component II, Crop Informatics, Genomics and Genetic Analyses, Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development, and 2B: Structural Comparison and Analysis of Crop Genomes. Progress on this project is monitored through written progress reports, email contacts and personal visits. During the reporting period we developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user. This software streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads, such as soybean. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations.