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SoyBase and the Soybean Breeder's Toolbox
Integrating Genetics and Molecular Biology for Soybean Researchers |
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This is the first version of the SoyCyc Soybean Metabolic Pathway Database. The data in this database were inferred by ab-initio methods from the Gm1.01 Glycine max Williams82 genome sequence gene calls from the Joint Genome Institute (JGI, Phytozome).
The first step in using the program is to select a database using the selector at the top right of the page. Clicking on "change" will drop down a selector window with a list of the available databases. The choices are:
| Database Name | Description |
|---|---|
| Glycine Max | The SoyCyc Database |
| Medicago truncatula | The MedicCyc Database (Noble Foundation, Sumner Lab) |
| PlantCyc | Compendium of all public plant MetaCyc Databases (PlantCyc Project) |
After highlighting your choice, click the "OK" button in the lower right of the window.
The second step is to choose an activity from the menu bar above.
The "Search" button allows you to search for information in a number of ways.
| Search By | Description |
|---|---|
| Compounds | Searches using compound names. |
| Genes/Proteins/RNAs | Searches using gene, protein or structural RNA names. |
| Reactions | Searches using biochemical reaction names. |
| Pathways | Searches using proper pathway names. |
| Advanced | Perform direct database queries. |
| Ontologies | Search for genes and pathway information using ontological terms from GO, EC, etc. |
The "Tools" button allows you access to a number of computational tools to examine the database.
| Tool | Description |
|---|---|
| Cellular Overview | Presents a schematic of known pathways and annotation data. |
| Omics Viewer | Annotate pathway information with data from transcriptomic experiments. |
| Comparative Analysis | Identify pathways in common between the available databases. |
| Reports | Generate descriptive reports for the database. |
