<html>
-<head><title>Alignment Consensus Annotation</title></head>
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+ -->
+<head>
+<title>Alignment Consensus Annotation</title>
+</head>
<body>
-<p><strong>Alignment Consensus Annotation</strong></p>
-<p>The consensus displayed below the alignment is the percentage of the modal
- residue per column. By default this calculation takes includes gaps in column.
- You can choose to ignore gaps in the calculation by right clicking on the label
- "Consensus" to the left of the consensus bar chart.
-<p>If the modal value is shared by more than 1 residue, a "+" symbol
- is used in the display for the simple reason that it is not possible to display
- multiple characters in a single character space.
-<p><strong>Copying the consensus sequence</strong></p>
-<p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
-the consensus annotation label to copy the alignment's consensus sequence to the
-clipboard.
-</p>
+ <p>
+ <strong>Alignment Consensus Annotation</strong>
+ </p>
+ <p>The consensus displayed below the alignment is the percentage
+ of the modal residue per column. By default this calculation
+ includes gaps in columns. You can choose to ignore gaps in the
+ calculation by right clicking on the label "Consensus" to
+ the left of the consensus bar chart.
+ <p>If the modal value is shared by more than 1 residue, a
+ "+" symbol is used in the display for the simple reason
+ that it is not possible to display multiple characters in a single
+ character space.
+ <p>
+ <strong>Copying the consensus sequence</strong>
+ </p>
+ <p>
+ Select the <strong>"Copy Consensus Sequence"</strong>
+ entry from the consensus annotation label to copy the alignment's
+ consensus sequence to the clipboard.
+ <p>
+ <strong>Sequence logo</strong>
+ </p>
+ By clicking on the label you can also activate the sequence logo. It
+ indicates the relative amount of residues per column which can be
+ estimated by its size in the logo. The tooltip of a column gives the
+ exact numbers for all occurring residues.
+ <br />If columns of the alignment are very diverse, then it can
+ sometimes be difficult to see the sequence logo - in this case, right
+ click on the annotation row label and select
+ <strong>Normalise Consensus Logo</strong> to scale all columns of the
+ logo to the same height.
+
+ <p>
+ <strong>cDNA Consensus</strong>
+ </p>
+ A
+ <a href="../features/splitView.html">Split Frame View</a> of cDNA and
+ Protein alignments will show the consensus for cDNA below the protein
+ alignment.
+ <br /> This may provide additional information on mutations in DNA
+ that is not visible in the peptide alignment.
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff