+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Split Frame Views</title>
-</head>
-<body>
- <p>
- <strong>Split Frame Views</strong>
- </p>
- <p>
- Jalview provides a special viewing mode to show Coding DNA (cDNA)
- and protein product alignments as a split view, with cDNA above and
- protein below. The two alignments are linked, allowing editing and
- analysis to be performed at both the peptide and nucleotide level.
- Linked protein alignments also have an additional <strong>cDNA
- Consensus</strong> annotation row, showing the distribution of codons at
- each column of the protein alignment.
- </p>
- <p>
- Split Frame views can be <a href="#opensplit">created in a
- number of ways</a>. In the Jalview Desktop, Split Frame views are
- saved in Jalview Projects, like any other alignment view.
- </p>
- <p>
- <strong>Operations supported in Split Frame Mode</strong>
- </p>
- <p>Split Frame views allow the following:
- <ul>
- <li>Mouseover or scrolling of either alignment is followed by
- the other (unless you turn off <strong><a
- href="../menus/alwview.html">"View→Automatic
- Scrolling"</a></strong>)
- </li>
- <li>On selecting rows, columns or regions in one alignment, the
- corresponding selection is made in the other</li>
- <li>Sequence ordering in one alignment (using the cursor, or <strong><a
- href="../calculations/sorting.html">"Calculate→Sort")</a></strong>
- is also applied to the other
- </li>
- <li>Editing (gap insertion / deletion) in the protein alignment
- is reflected in the cDNA (but not vice versa)</li>
- <li>Any trees imported or created with <strong><a
- href="../calculations/tree.html">"Calculate Tree"</a></strong> on
- one of the views allow both cDNA and Protein views to be grouped,
- coloured or sorted.
- </li>
- <li>To allow for the different widths in cDNA and Protein
- alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
- menu option has an option 'Scale protein residues to codons'. This
- option will make each protein residue the same width as a DNA
- codon (so the alignments 'line up' vertically).<br/><br/>
- <a name="mirror"/>The 'Use same
- font for cDNA and peptide' checkbox, when enabled, ensures that font or
- font-size changes in either the cDNA or Protein alignment will also
- be mirrored. (<em>Added in 2.10.2</em>)
- </li>
- <li><strong>"View→Protein"</strong> (in the cDNA panel)
- or <strong>"View→Nucleotide"</strong> (in the protein panel)
- allows you to show or hide one or other of the linked alignment
- panels.</li>
- <li>Panel heights are adjusted dragging the divider between
- them using the mouse</li>
- <li><a href="../menus/alwview.html"><strong>"View→New
- View / Expand Views / Gather Views"</strong></a> behave as for a normal
- alignment window, but always create new views as Split Frames</li>
- </ul>
- <p>
- An alignment annotation row on the protein alignment shows the <strong><a
- href="../calculations/consensus.html">cDNA consensus</a></strong> for
- each peptide column.<br /> This consensus may reveal variation in
- nucleotides coding for conserved protein residues.
- </p>
-
- <a name="opensplit" />
- <p>
- <strong>Opening a Split Frame View</strong>
- </p>
- <p>A Split Frame View can be opened in one of the following ways:</p>
- <p>
- <strong><em>Add Sequences</em></strong>
- </p>
- <p>
- If you add (coding) DNA sequences to an open peptide alignment, or
- vice versa, <em>and</em> at least one DNA sequence translates to one
- of the peptide sequences, then the option to open in a split window
- is offered. The DNA may include start and/or stop codons, but no
- non-coding (intron) sequence.<br> If more than one cDNA variant
- is present in the alignment, Jalview will first try to match these
- to protein sequences based on any retrieved cross-references, and
- failing that, pairwise as they are ordered in the alignments.
- <p>This option is available in Jalview Desktop (when adding
- sequences by any supported method), and Jalview applet (adding from
- textbox). The additional options below apply to Jalview Desktop
- only.</p>
-
- <p>
- <strong><em>Translate as cDNA</em></strong>
- </p>
- <p>
- Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Translate
- as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this
- option shows the DNA and its calculated protein product in a Split
- Frame view.
- </p>
-
- <p>
- <strong><em>Get Cross-References</em></strong>
- </p>
- <p>
- Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Get
- Cross-References"</a></strong> is available for fetched sequences which have
- cross-references to other databases. On selecting protein
- cross-references (for a cDNA alignment), or DNA xrefs (for peptide),
- a Split Frame view is opened showing cDNA and peptide.
- </p>
-
- <p>
- <strong><em>Realign a Split View</em></strong>
- </p>
- <p>If you invoke a web service to realign either half of a Split
- Frame, then the resulting realignment is displayed in a new Split
- Frame.</p>
- <ul>
- <li>the alignment you chose to realign (for example, peptide)
- is displayed as aligned by the external web service</li>
- <li>Jalview reconstructs the alignment of its complement (in
- this case, cDNA) by inserting gaps in the corresponding positions</li>
- </ul>
- <p>
- <a name="reconalignment" /><strong>Reconstructed
- Alignments</strong>
- </p>
- <p>
- Reconstructed alignments are typically <em>not</em> the same as the
- alignment produced by aligning the complement sequence set directly
- with the external service. However, in the case of protein
- alignments, a reconstructed cDNA alignment is often more reliable
- than one calculated without coding information. Reconstructed cDNA
- alignments are also more informative than the original protein
- alignment when calculating phylogenetic trees or performing other
- kinds of molecular evolution analysis.
- </p>
- <p>
- <em>Split Frame Views were introduced in Jalview 2.9</em>
- </p>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff