+++ /dev/null
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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
- 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>Group Consensus</strong><br>
- If sequence groups have been defined, then selecting option 'Group Consensus' in the <a href="../menus/alwannotation.html">Annotations menu</a> will
- result in Consensus being calculated for each group, as well as the alignment as a whole.
- </p>
- <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