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23 <title>Reference Sequences</title>
27 <strong>Reference Sequence Alignment Views</strong>
29 <p>Many alignment analysis tasks concern a query, or reference
30 sequence. For instance, when searching for sequences from other
31 organisms that are similar to a newly sequenced gene, or when
32 searching for structurally similar sequences for use in homology
35 <strong>What happens when a reference sequence is defined ?</strong>
38 The reference sequence for an alignment is indicated by its ID being
39 shown in bold. In addition:</p>
41 <li><strong>Reference sequence numbering</strong>. Instead of
42 column numbers, the alignment ruler shows the reference sequence
43 positions at each column. At each tick mark, either the reference
44 sequence symbol and position is given, or the column number when a
45 gap is present at that position in the reference sequence.</li>
46 <li><strong>Format→Show unconserved</strong> highlights
47 mutations with respect to the reference sequence, rather than the
48 alignment's consensus sequence.</li>
51 <strong>Defining the reference sequence</strong>
53 <p>Each alignment view can have its own reference sequence.</p>
55 <li><strong>Manually assigning a reference sequence</strong><br />
56 A sequence can be marked as the reference sequence by
57 right-clicking on its ID to open the popup menu, and selecting the
58 "<strong>(Sequence ID)→Mark as Reference</strong>" entry.</li>
59 <li><strong>Defining a reference when importing
60 annotation</strong><br />Jalview automatically assigns a reference
61 sequence when importing analysis results, such as those returned
62 from <a href="../webServices/jnet.html">JPred4</a> . A reference
63 sequence can also be assigned via the <a
64 href="../features/annotationsFormat.html#refsandviews">SET_REF</a> command in
65 an alignment annotation file.</li>
68 <em>Reference sequence based alignment visualisation was
69 introduced in Jalview 2.9, and support for storage and retrieval
70 of reference sequence views in 2.10.</em>