- <li>Jalview automatically assigns a reference sequence when <a
- href="../webServices/jnet.html"
- >JPred4</a> predictions are imported.
- </li>
- <li><strong>Assigning a reference sequence</strong><br /> A
- sequence can be marked as the reference sequence by right-clicking
- on it's ID to open the popup menu, and selecting the "<strong>(Sequence
- ID)→Mark as Reference</strong>" entry."</li>
+ <li><strong>Manually assigning a reference sequence</strong><br />
+ A sequence can be marked as the reference sequence by
+ right-clicking on its ID to open the popup menu, and selecting the
+ "<strong>(Sequence ID)→Mark as Reference</strong>" entry.</li>
+ <li><strong>Defining a reference when importing
+ annotation</strong><br />Jalview automatically assigns a reference
+ sequence when importing analysis results, such as those returned
+ from <a href="../webServices/jnet.html">JPred4</a> . A reference
+ sequence can also be assigned via the <a
+ href="../features/annotationsFormat.html#refsandviews">SET_REF</a> command in
+ an alignment annotation file.</li>