Data Mining and Analysis at SoyBase

SoyBase, the USDA-ARS soybean genetics and genomics database, provides a number of data mining and analysis tools. While some of these will be familiar to most users, many are unique to SoyBase. This poster will highlight some of the tools available at SoyBase. Other tools not listed here will also be covered in the poster.

Affymetrix SoyChip1 Browser: Annotations for the chip contig sequences can be searched or downloaded. Unigenes with exact matches to the contig sequences can be identified. All locations of the chip contig sequences in the Wm82 sequence can be visualized.

SoyCyc: This metabolism database and visualization tool is based on the Wm82 gene calls and MetaCyc pathways. Several search tools are provided along with a comprehensive metabolism overview diagram.

Fast Neutron Mutants: Several innovative tools are provided for identifying mutants of interest including a searchable collection of plant images, BLAST homology searches against the indel sequences, searching of the mutants by any combination of seed composition or plant architecture trait values and identification of indel(s) that overlap one or more genes of interest. The genes covered by the indels can also be visualized as a distinct subset of the pathways in SoyCyc.

Gene Expression: The SoyBase genome browser has tracks that show gene expression from several legume species under a number of experimental conditions. A RNA-Seq gene atlas for soybean covering 14 tissues and developmental time-points is presented. A number of tools for searching the atlas or visualization of the expression patterns are provided.