Help Home > Simple Search > Searching for Gene Model Hits to Multiple Databases

Searching for Gene Model Hits to Multiple Databases

With this search you can find JGI-predicted genes (gene models) whose translated sequences have Smith-Waterman alignments with proteins in a variety of relevant public databases. To launch this search, use only the Gene Model Hits form.

1. Make sure the Smith-Waterman radio button is selected.
2. From the first pull-down menu, select a field from the external database to search. The options are Hit Id, Hit Name (nearly always the same as the Hit Id), and Hit Description.
3. In the contains text box, type your search term (e.g., 20302 for a hit ID or hit name, H+ ATPase for a hit description).
4. From the second pull-down menu, select the statistical criteria you would like to use to limit the results, either score or E-value.
5. In the text box, type the E-value or score you want to use as the cutoff (e.g., 900 for a score, 1e-25 for an E-value.
6. In the Taxonomy contains text box, type any taxonomic term to which you want to limit results (e.g., oryza).
7. Choose a database (or All) from the Database equals menu.
8. Choose a sort option from the sort by menu. The options are Score, E-value, or Protein Id.
9. Click Search Hits.

Results from Searches for Hits to Multiple Databases