<pre>GROUP_REF	<em>ALIGNMENT</em></pre>
</p>
<hr/>
-<p><strong><a name="refsandviews">VIEW_SETREF, VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br/>
-Since Jalview 2.9, the Annotations file has also supported the definition of reference sequences and hidden regions for an alignment view.</p>
-<!-- <p>
+ <p>
+ <strong><a name="refsandviews">VIEW_SETREF,
+ VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br /> Since Jalview 2.9, the
+ Annotations file has also supported the definition of reference
+ sequences and hidden regions for an alignment view.
+ </p>
+ <!-- <p>
<em>VIEW_DEF</em> allows the current view to be named according to the
first argument after the tab character. If a second argument is
provided, then a new view is created with the given name, and
properties.
</p> -->
- <p>
- <em>VIEW_SETREF</em> marks the first sequence in the alignment, or
- alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
- statement, as the <a href="../features/refsequence.html">reference
- sequence</a> for the alignment.
- </p>
- <p>
- <em>HIDE_INSERTIONS</em>This command hides all gapped positions in the
- current target sequence. Any columns already hidden will be
- re-displayed.<br />
- <br>The current target sequence is either the one specified by
- the most recent <em>SEQUENCE_REF</em> statement, the alignment's
- reference sequence, or the first sequence in the alignment.
- </p>
- <p>
- <em>VIEW_HIDECOLS</em> modifies the visibility of columns in the view.
- The statement is followed by a single argument consisting of a comma
- separated series of single integers or integer pairs (like <em>3-4</em>).
- These define columns (starting from the left-hand column 0) that
- should be marked as hidden in the alignment view.
- </p>
+ <p>
+ <em>VIEW_SETREF</em><br />Marks the first sequence in the alignment,
+ or alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, as the <a href="../calculations/referenceseq.html">reference
+ sequence</a> for the alignment.
+ </p>
+ <p>
+ <em>HIDE_INSERTIONS</em><br />This command hides all gapped
+ positions in the current target sequence. Any columns already hidden
+ will be re-displayed.<br /> <br>The current target sequence is
+ either the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, the alignment's reference sequence, or the first sequence
+ in the alignment.
+ </p>
+ <p>
+ <em>VIEW_HIDECOLS</em><br />Modifies the visibility of columns in
+ the view. The statement is followed by a single argument consisting
+ of a comma separated series of single integers or integer pairs
+ (like <em>3-4</em>). These define columns (starting from the
+ left-hand column 0) that should be marked as hidden in the alignment
+ view.
+ </p>
- <hr/>
-<p><strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br/>
+ <hr />
+ <p><strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br/>
The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
so that only annotation line graphs with the given names ands the same
<strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</p>
</p>
Jalview can be used to view protein structures by following the steps below:
<ol>
- <li>Select the <strong>"View Structure"</strong> option from a
- sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
+ <li>Select the <strong>"3D Structure Data..."</strong> option from a
+ sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to open the <a href="structurechooser.html">Structure Chooser</a> dialog box.
<ul>
<li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
- dialogue is opened with a list of the found structures meta-data.</li>
- <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
+ dialog will open with them listed in the results pane.</li>
+ <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface will present options for manual association of PDB structures.</li>
</ul>
</li>
- <li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
- on the desired structure(s) in the list, or automatically by
- using the drop-down menu on the interface to filter and auto-select the best structure based on certain
- criteria like quality, resolution, etc.</li>
- <li>When the desired structure(s) have been selected, they can be
- viewed by clicking the <strong>"View"</strong> button below the summary list.
- </li>
-
- </ol>
+ <li><strong>Selecting Structures</strong><br /> If structures
+ have been discovered, then some will already be selected according
+ to predefined selection criteria, such as structures with the
+ highest resolution. Use the drop down menu to select structures
+ according to different criteria, or, alternatively, choose
+ structures manually by selecting with the keyboard and mouse.
+ <ul>
+ <li><strong>Viewing Cached Structures</strong><br />If you
+ have previously downloaded structures for your sequences, they
+ can be viewed by selecting the <strong>Cached PDB
+ Entries</strong> option from the drop down menu at the top of the
+ dialog box.</li>
+ </ul></li>
+ <li>To view selected structures, click the <strong>"View"</strong>
+ button.
+ </li>
+ </ol>
The
<a href="jmol.html">Jmol viewer</a> has been included since Jalview
href="xsspannotation.html">Annotation from Structure</a> page for
more information.
</p>
- <!--
- <p>The following menu entries are provided for viewing structure data
- <ul>
- <li>The <strong>"Structure→View
- Structure→</strong> submenu allows a single PDB structure to be chosen
- for display from the available structures for a sequence.
- </li>
- <li>The <strong>"Structure→View all <em>N</em>
- structures
- </strong> option will open a new window containing all structures associated
- with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
- capability was added in Jalview 2.7</em>
- </li>
- <li>The <strong>"Structure→View all <em>N</em>
- representative structures
- </strong> option will open a new window containing exactly one structure per
- currently selected sequence.<br />
- <em>The View representative structures option was introduced in
- Jalview 2.8.1</em></li>
- </ul>
-</p> -->
-<p>If a <strong>single</strong> pdb
+<p>If a <strong>single</strong> PDB
structure is selected, one of the following will happen:</p>
<ul>
entry. For PDB sequences, simply select PDB as the database and enter
your known PDB id (appended with ':' and a chain code, if desired).<br>
Jalview will also read PDB files directly. Simply load in the file as
-you would an alignment file. The sequences of any peptide chains will be
+you would an alignment file. The sequences of any protein or nucleotide chains will be
extracted from the file and viewed in the alignment window.</p>
<p>
</head>
<body>
- <p>
- <strong>Alignment Window Menus</strong>
- </p>
- <ul>
+ <!-- NOTE: THIS PAGE COLLECTS TOGETHER THE INDIVIDUAL ALIGNMENT WINDOW MENU PAGES - DON"T EDIT INDIVIDUAL ENTRIES HERE! -->
+ <p>
+ <strong>Alignment Window Menus</strong>
+ </p>
+ <ul>
<li><strong>File</strong>
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows a
<li><strong>Phylip</strong></li>
<li><strong>JSON</strong></li>
</ul></li>
- <li><strong>Print (Control P)<br> </strong><em>Jalview
- will print the alignment using the current fonts and colours of
- your alignment. If the alignment has annotations visible, these
- will be printed below the alignment. If the alignment is wrapped
- the number of residues per line of your alignment will depend on
- the paper width or your alignment window width, whichever is the
- smaller. </em>
- </li>
- <li><strong>Export Image</strong> <em><br> Creates an
- alignment graphic with the current view's annotation, alignment
- background colours and group colours. If the alignment is <a
- href="../features/wrap.html">wrapped</a>, the output will also be
- wrapped and will have the same visible residue width as the open
- alignment. </em>
- <ul>
- <li><strong>HTML<br> </strong><em>Create a <a
- href="../io/export.html">web page</a> from your alignment.</em>
- </li>
- <li><strong>EPS<br> </strong><em>Create an <a
- href="../io/export.html">Encapsulated Postscript</a> file from
- your alignment.</em>
- </li>
- <li><strong>PNG<br> </strong><em>Create a <a
- href="../io/export.html">Portable Network Graphics</a> file from
- your alignment.</em>
- </li>
- </ul></li>
- <li><strong>Export Features</strong><em><br> All
+<li><strong>Page Setup ...</strong><br>
+ <em>Open the printing system's Page Setup dialog box, to
+ control page size, layout and orientation.</em></li>
+ <li><strong>Print (Control P)<br>
+ </strong><em>Jalview will print the alignment using the current fonts and
+ colours of your alignment. If the alignment has annotations visible,
+ these will be printed below the alignment. If the alignment is wrapped
+ the number of residues per line of your alignment will depend on the
+ paper width or your alignment window width, whichever is the smaller. </em></li>
+ <li><strong>Export Image</strong> <em><br>
+ Creates an alignment graphic with the current view's annotation,
+ alignment background colours and group colours. If the alignment is <a
+ href="../features/wrap.html">wrapped</a>, the output will also be
+ wrapped and will have the same visible residue width as the open
+ alignment. </em>
+ <ul>
+ <li><strong>HTML<br>
+ </strong><em>Create a <a href="../io/export.html">web page</a> from your
+ alignment.</em></li>
+ <li><strong>EPS<br>
+ </strong><em>Create an <a href="../io/export.html">Encapsulated
+ Postscript</a> file from your alignment.</em></li>
+ <li><strong>PNG<br>
+ </strong><em>Create a <a href="../io/export.html">Portable Network
+ Graphics</a> file from your alignment.</em></li>
+ <li><strong>SVG<br>
+ </strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
+ <li><strong>BioJS<br>
+ </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
+ </ul>
+ </li>
+ <li><strong>Export Features</strong><em><br> All
features visible on the alignment can be saved to file or
displayed in a textbox in either Jalview or GFF format</em>
</li>
annotations</a>.</em></li>
<li><strong>Close (Control W)</strong><br> <em>Close
the alignment window. Make sure you have saved your alignment
- before you close - either as a Jalview project or by using the <strong>Save
+ before you close - either from the Desktop's <strong>Save Project</strong> File menu option, or by using the <strong>Save
As</strong> menu.</em>
</li>
</ul></li>
</ul></li>
<li><strong>Select</strong>
<ul>
- <li><strong><a href="../features/search.html">Find...
- (Control F)</a> </strong><em><br> Opens the Find dialog box to
- search for residues, sequence name or residue position within the
- alignment and create new sequence features from the queries. </em>
- </li>
- <li><strong>Select All (Control A)<br> </strong><em>Selects
- all the sequences and residues in the alignment. <br> Use
- <CTRL> and A (<APPLE> and A on a MacOSX) to select
- all.</em></li>
- <li><strong>Deselect All (Escape)<br> </strong><em>Removes
- the current selection box (red dashed box) from the alignment
- window. All selected sequences, residues and marked columns will
- be deselected. </em><em> <br> Use <ESCAPE> to deselect
- all.</em></li>
- <li><strong>Invert Sequence Selection (Control I)<br>
- </strong><em>Any sequence ids currently not selected will replace the
- current selection. </em>
- </li>
- <li><strong>Invert Column Selection (Control Alt I)<br>
- </strong><em>Any columns currently not selected will replace the current
- column selection. </em>
- </li>
- <li><strong>Create Group (Control G)<br></strong>
- <em>Create a group containing the currently selected sequences.</em></li>
+ <li><a href="../features/search.html"><strong>Find... (Control F)</strong></a><br>
+ <em>Opens the Find dialog box to search for residues, sequence name or residue
+ position within the alignment and create new sequence features from the queries.
+ </em>
+ <li><strong>Select All (Control A)</strong><strong><br>
+ </strong><em>Selects all the sequences and residues in the alignment. <br>
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></em></li>
+ <li><strong>Deselect All (Escape)<br>
+ </strong><em>Removes the current selection box (red dashed box) from the
+ alignment window. All selected sequences, residues and marked columns
+ will be deselected. </em><em> <br>
+ Use <ESCAPE> to deselect all.</em></li>
+ <li><strong>Invert Sequence Selection (Control I)<br>
+ </strong><em>Any sequence ids currently not selected will replace the
+ current selection. </em></li>
+ <li><strong>Invert Column Selection (Control Alt I)<br>
+ </strong><em>Any columns currently not selected will replace the current
+ column selection. </em></li>
+ <li><strong>Create Group (Control G)<br></strong>
+ <em>Create a group containing the currently selected sequences.</em></li>
<li><strong>Remove Group (Shift Control G)<br></strong>
- <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
- <li><strong>Make Groups for selection<br /> </strong> <em>The currently
- selected groups of the alignment will be subdivided according to
- the contents of the currently selected region. <br />Use this to
- subdivide an alignment based on the different combinations of
- residues observed at specific positions. (new in Jalview 2.5)</em>
- </li>
- <li><strong>Undefine Groups (Control U)<br> </strong><em>The
- alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
- This cannot be undone.</em>
- </li>
+ <em>Ungroup the currently selected sequence group.</em></li>
+ <li><strong>Make Groups for selection<br /></strong> <em>The
+ currently selected groups of the alignment will be subdivided
+ according to the contents of the currently selected region. <br />Use
+ this to subdivide an alignment based on the different combinations
+ of residues at marked columns.
+ </em></li>
+ <li><strong>Undefine Groups (Control U)<br>
+ </strong><em>The alignment will be reset with no defined groups.<br>
+ <strong>WARNING</strong>: This cannot be undone.</em></li>
+ <li><strong><a
+ href="../features/columnFilterByAnnotation.html">Select/Hide Columns by Annotation</a></strong> <br />
+ <em>Select or Hide columns in the alignment according to
+ secondary structure, labels and values shown in alignment
+ annotation rows. </em></li>
</ul></li>
<li><strong>View</strong>
<ul>
</li>
</ul>
</li>
- <li><strong>Calculate Tree </strong> <br> <em>Functions
- for calculating trees on the alignment or the currently selected
- region. See <a href="../calculations/tree.html">calculating
- trees</a>.</em>
- <ul>
- <li><strong>Average Distance Using % Identity</strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Neighbour Joining Using Blosum62<br>
- </strong></li>
- </ul>
- <strong>Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.</strong>
- </li>
+ <li><strong>Calculate Tree </strong> <br> <em>Functions
+ for calculating trees on the alignment or the currently
+ selected region. See <a href="../calculations/tree.html">calculating
+ trees</a>.
+ </em>
+ <ul>
+ <li><strong>Neighbour Joining Using PAM250 </strong></li>
+ <li><strong>Neighbour Joining Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Neighbour Joining Using Blosum62 </strong></li>
+ <li><strong>Neighbour Joining Using % Identity</strong></li>
+ <li><strong>Average Distance Using PAM250 </strong></li>
+ <li><strong>Average Distance Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Average Distance Using Blosum62</strong></li>
+ <li><strong>Average Distance Using % Identity</strong></li>
+ </ul> <strong>Note: Since Version 2.8.1, a number of
+ additional similarity measures for tree calculation are
+ provided in this menu.</strong></li>
<li><strong>Pairwise Alignments</strong><br> <em>Applies
Smith and Waterman algorithm to selected sequences. See <a
href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
<em>This menu is opened by clicking anywhere on the annotation row labels
area (below the sequence ID area).</em>
<ul>
- <li><strong> Add New Row</strong><br>
+ <li><strong>Add New Row</strong><br>
<em>Adds a new, named annotation row (a dialog box will pop up for you
to enter the label for the new row). </em> </li>
<li><strong>Edit Label/Description</strong><br>
<ul>
<li><strong>Sort </strong>
<ul>
- <li><strong>by ID</strong><em><br> This will sort the
+ <li><strong>By ID</strong><em><br> This will sort the
sequences according to sequence name. If the sort is repeated, the
order of the sorted sequences will be inverted. </em>
</li>
- <li><strong>by Length</strong><em><br> This will sort
+ <li><strong>By Length</strong><em><br> This will sort
the sequences according to their length (excluding gap
characters). If the sort is repeated, the order of the sorted
sequences will be inverted. </em>
</li>
- <li><strong>by Group</strong><strong><br> </strong><em>This
+ <li><strong>By Group</strong><strong><br> </strong><em>This
will sort the sequences according to sequence name. If the sort is
repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
</li>
- <li><strong>by Pairwise Identity<br> </strong><em>This
+ <li><strong>By Pairwise Identity<br> </strong><em>This
will sort the selected sequences by their percentage identity to
the consensus sequence. The most similar sequence is put at the
top. </em>
associated score annotation, or you have just done a multiple
alignment calculation or opened a tree viewer window.</em><br></li>
</ul></li>
- <li><strong>Calculate Tree </strong> <br> <em>Functions
- for calculating trees on the alignment or the currently selected
- region. See <a href="../calculations/tree.html">calculating
- trees</a>.</em>
- <ul>
- <li><strong>Average Distance Using % Identity</strong>
- </li>
- <li><strong>Neighbour Joining Using % Identity</strong>
- </li>
- <li><strong>Average Distance Using Blosum62</strong>
- </li>
- <li><strong>Neighbour Joining Using Blosum62<br>
- </strong>
- </li>
- </ul></li>
- <li><strong>Pairwise Alignments</strong><br> <em>Applies
+ <li><strong>Calculate Tree </strong> <br> <em>Functions
+ for calculating trees on the alignment or the currently selected
+ region. See <a href="../calculations/tree.html">calculating
+ trees</a>.
+ </em>
+ <ul>
+ <li><strong>Neighbour Joining Using PAM250<br>
+ </strong></li>
+ <li><strong>Neighbour Joining Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Neighbour Joining Using Blosum62<br>
+ </strong></li>
+ <li><strong>Neighbour Joining Using % Identity</strong></li>
+ <li><strong>Average Distance Using PAM250<br>
+ </strong></li>
+ <li><strong>Average Distance Using Sequence
+ Feature Similarity</strong></li>
+ <li><strong>Average Distance Using Blosum62</strong></li>
+ <li><strong>Average Distance Using % Identity</strong></li>
+ </ul></li>
+ <li><strong>Pairwise Alignments</strong><br> <em>Applies
Smith and Waterman algorithm to selected sequences. See <a
href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
</li>
<li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See <a href="../calculations/pca.html">Principal
+ a spatial clustering of the sequences based on similarity scores calculated over the alignment.. See <a href="../calculations/pca.html">Principal
Component Analysis</a>.</em> <br></li>
<li><strong>Extract Scores ... (optional)</strong><br> <em>This
option is only visible if Jalview detects one or more white-space
this option is selected, the alignment will be automatically sorted
whenever a new tree is calculated or loaded.</em> <br>
</li>
- </ul>
+ <li><strong>Show Flanking Regions</strong><br> <em>Opens
+ a new alignment window showing any additional sequence data
+ either side of the current alignment. Useful in conjunction with
+ 'Fetch Database References' when the 'Trim Retrieved Sequences'
+ option is disabled to retrieve full length sequences for a set
+ of aligned peptides. </em></li>
+ </ul>
</body>
</html>
<li><strong>Create Group (Control G)<br></strong>
<em>Create a group containing the currently selected sequences.</em></li>
<li><strong>Remove Group (Shift Control G)<br></strong>
- <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
+ <em>Ungroup the currently selected sequence group.</em></li>
<li><strong>Make Groups for selection<br /></strong> <em>The
currently selected groups of the alignment will be subdivided
according to the contents of the currently selected region. <br />Use
this to subdivide an alignment based on the different combinations
- of residues at marked columns. (since Jalview 2.9)
+ of residues at marked columns.
</em></li>
<li><strong>Undefine Groups (Control U)<br>
</strong><em>The alignment will be reset with no defined groups.<br>
<strong>WARNING</strong>: This cannot be undone.</em></li>
- <li><strong>Select/Hide Columns by Annotation...</strong> <br/><em>Select or hide columns of an alignment by filtering with properties of any annotation row added to that alignment</em></li>
-
-</ul>
+ <li><strong><a
+ href="../features/columnFilterByAnnotation.html">Select/Hide Columns by Annotation</a></strong> <br />
+ <em>Select or Hide columns in the alignment according to
+ secondary structure, labels and values shown in alignment
+ annotation rows. </em></li>
+ </ul>
</body>
</html>
<li><strong>Gather Views (G)</strong><em><br>
Each view associated with the alignment will be displayed within its own tab
on the current alignment window. </em></li>
- <li><strong>Show→(all Columns / Sequences / Sequences and Columns</strong> )</strong><em><br>
+ <li><strong>Show→(all Columns / Sequences / Sequences and Columns</strong>)</strong><em><br>
All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
<li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region)</strong><em><br>
Hides the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
Annotations<br>
</strong><em>When enabled, copies any available alignment annotation
for this sequence to the current view.</em></li>
+ <li><strong>Set as Reference</strong> or <strong>Unmark as Reference</strong><br/>
+ Sets or unsets the reference sequence for the the alignment.
+ </li>
+
<li><strong>Represent Group With (Sequence Id)</strong><br>
<em>All sequences in the current selection group will be
hidden, apart from (Sequence Id). Any edits performed on the
href="../features/varna.html">VARNA</a>.
</em>
</li>
-<!--
- <p>
- <em>Other menu entries may also be shown if the current
- selection includes sequences with associated structure data:</em><br>
- <ul>
- <li><strong>Associate Structure with Sequence</strong>
- <ul>
- <li><strong>From File<br>
- </strong><em>Load a PDB file from local disk which will be associated
- with this sequence. This file will be used if the user subsequently
- clicks on "View Structure" menu item.</em></li>
- <li><strong>Enter PDB id<br>
- </strong><em>Enter the PDB id from an input window. This PDB id will
- be used by the service WSDBFetch, provided by the EBI, to fetch the
- PDB file if the user subsequently clicks on its "View Structure"
- menu item. </em></li>
- <li><strong>Discover PDB ids<br>
- </strong><em>This will use the service WSDBFetch, provided by the
- EBI, to retrieve all PDB ids associated with the sequences in the
- alignment if the sequences have valid Uniprot names or accession ids.
- </em></li>
- </ul>
- </li>
-
- <ul>
- <li><strong>Structure→View all <em>N</em>
- structures<br />
- </strong><em>Opens a new window containing all structures associated
- with the current selection, superposed according to the currently
- selected region of the alignment.<br />(This capability was
- added in Jalview 2.7)
- </em></li>
- <li><strong>Structure→View all <em>N</em>
- representative structures<br />
- </strong><em>Open a new window containing exactly one structure per
- currently selected sequence.<br /> (The View representative
- structures option was introduced in Jalview 2.8.1)
- </em></li>
- </ul>
- <br> -->
-
- <li><strong>Hide Sequences</strong><br> <em>Hides the
+ <li><strong>Hide Insertions</strong><br />
+ <em>Hides columns containing gaps in the current sequence or
+ selected region, and reveals columns not including gaps.</em>
+ <li><strong>Hide Sequences</strong><br> <em>Hides the
currently selected sequences in this alignment view.</em><strong><br>
</strong></li>
</ul>
</head>
<body>
<strong>JNet Secondary Structure Prediction</strong>
-<p>Secondary structure prediction methods attempts to infer the
-likely secondary structure for a protein based on its amino acid
-composition and similarity to sequences with known secondary structure.
-The JNet method uses several different neural networks and decides on
-the most likely prediction via a jury network. <br>
-<ul>
+<p>
+ Secondary structure prediction methods attempts to infer the likely
+ secondary structure for a protein based on its amino acid
+ composition and similarity to sequences with known secondary
+ structure. The most recent version of the method, JPred4, employs a
+ series of neural networks trained to predict different secondary
+ structure types from a sequence profile, and when necessary, employs
+ a jury network to identify the most likely secondary structure
+ prediction.<br><ul><li>Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)<br/>
+JPred4: a protein secondary structure prediction server<br/>
+<em>Nucleic Acids Research</em>, <strong>Web Server issue</strong> (first published 15th April 2015)<br/>
+<a href="http://dx.doi.org/10.1093/nar/gkv332">http://dx.doi.org/10.1093/nar/gkv332</a>
+ </li>
<li>Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
secondary structure prediction server <em>Nucleic Acids Research</em> <strong>36</strong>
W197-W201</li>
git://source.jalview.org / jalview.git / commitdiff