Uniprot Free Text Search not working in Jalview (and earlier)

Due to an update at uniprot.org, Jalview’s Uniprot search interface has stopped working. Instead of showing the results of your query, a flashing yellow triangle next to the input box is shown instead.

We will shortly be releasing a new patch release that provides a fix for this problem, but until then, if you have an urgent need to access Uniprot’s free text search via Jalview, there is a workaround:

  1. First shutdown Jalview, then locate your .jalview_properties file and open it in a text editor (notepad on windows, or text wrangler on Macs, for instance).
  2. Make a new line and enter the following:


  1. Save your updated .jalview_properties file and then start Jalview. The Uniprot Search dialog should now be working: