Rfam web service (temporary) workaround

Jalview Discussion
1

The RFAM (Seed) new sequence fetcher is temporarily not working in Jalview. This will be fixed in the next update (which should apply to your installation automatically when it’s available).

In the meantime, if you require access to Rfam alignments you can either

  • Add the line
    RFAM_BASEURL=https\://rfam.org
    to your ~/.jalview_properties file (when Jalview is not running), and Jalview’s sequence fetcher should work subsequent times you launch Jalview; or

  • Download the alignment directly from https://rfam.org/family/ACCESSIONID/alignment/stockholm?download=1
    replacing ACCESSIONID with the appropriate identifier,
    e.g. https://rfam.org/family/RF00014/alignment/stockholm?download=1
    and load the downloaded file into Jalview (File → Input Alignment → From File).

Any problems with either of these, please feel free to ask below!

Ben