organisms that are similar to a newly sequenced gene, or when
searching for structurally similar sequences for use in homology
modelling.</p>
-<p>
+ <p>
<strong>What happens when a reference sequence is defined ?</strong>
</p>
- <p>
- The reference sequence for an alignment is indicated by its ID being
- shown in bold. In addition:</p>
+ <p>The reference sequence for an alignment is indicated by its ID
+ being shown in bold. In addition:</p>
<ul>
<li><strong>Reference sequence numbering</strong>. Instead of
column numbers, the alignment ruler shows the reference sequence
<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
+ from <a href="../webServices/jnet.html">JPred</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>
+ href="../features/annotationsFormat.html#refsandviews">SET_REF</a>
+ command in an alignment annotation file.</li>
</ul>
<p>
<em>Reference sequence based alignment visualisation was