This module displays SSR (simple sequence repeat) data. It assumes you have identified SSRs in your data and would like to annotate your features with these SSRs.
Generating data
SSRs can be predicted using these script. Alternatively SSRs can be experimentally determined and put into a spreadsheet that meets the criteria below.
Loading data
SSR data is loaded using a TripalImporter.
The Importer expects a tab-delimited file on the server with the following 9 columns:
| column | description |
|---|---|
| feature | Feature name that contain the SSR |
| motif | The repeat motif or base pattern that i repeated. For example, AT |
| repeats | How many times the motif is repeated |
| start | Start location in the parent feature |
| end | End location in the parent feature |
| fprimer | A forward primer to amplify the SSR |
| rprimer | A reverse primer to amplify the SSR |
| ftm | The forward primer's calculated Tm |
| rtm | The reverse primer's calculated Tm |
| size | The expected size of the PCR product |
Tripal 3
Features
The current master branch is compatible with Tripal 3. featureprops are automatically migrated as fields in the tripal ontology (ie. tripal__tripal_ssr_motif): to ensure they appear on your feature page, go to Structure->Tripal Content Type -> [feature of interest: ie, Gene], and click + Check for New Field. The terms should appear, and can be organized within their own pane by clicking on Manage Display.
Organisms
A new Field, so__microsatellite, is introduced for the Organism bundle. Navigate to Structure->Tripal Content Type -> Organism, and click + Check for New Field. The organism field instance provide a count of the SSRs for that organism, and a link to the SSR view for that organism providing a list of all feature and a bulk download option.