<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.
+ 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
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 occuring residues.
+ 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
<p><strong>About PCA</strong></p>
<p>Principal components analysis is a technique for examining the
structure of complex data sets. The components are a set of dimensions
-formed from the measured values in the data set, and the principle
+formed from the measured values in the data set, and the principal
component is the one with the greatest magnitude, or length. The sets of
measurements that differ the most should lie at either end of this
-principle axis, and the other axes correspond to less extreme patterns
+principal axis, and the other axes correspond to less extreme patterns
of variation in the data set.</p>
<p>
The PID option colours the residues (boxes and/or text) according to the percentage
of the residues in each column that agree with the consensus sequence. Only
the residues that agree with the consensus residue for each column are coloured.</p>
+<div align="center">
<table width="200" border="1">
<tr>
<td bgcolor="#6464FF">> 80 %</td>
<td>< 40%</td>
</tr>
</table>
+</div>
</body>
</html>
</p>
<p><em>Current Limitations</em></p>
<p>As of version 2.5, the Jalview user interface does not support the
-creation and editing quantitative annotation (histograms and line graphs), or
+creation and editing of quantitative annotation (histograms and line graphs), or
to create annotation associated with a specific sequence. It is also incapable of
annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an
<a href="annotationsFormat.html">Annotation file</a>.<br>
</td>
<td>Set the colourscheme for the alignment. This can be any of
the built-in colourschemes, a name of a predefined colourscheme
- (defined in the jalview properties file), or an 'inline' colourscheme
+ (defined in the Jalview properties file), or an 'inline' colourscheme
(see the applet's colour parameter for more information).</td>
</tr>
<tr>
<p>When the DAS Settings panel is first opened, and when the <strong>'Refresh
source'</strong> buton is pressed, a list of DAS sources is retrieved from the
DAS registry URL (set by default to the DAS registration server at
-http://das.sanger.ac.uk/registry/das1/sources/).</p>
+http://www.dasregistry.org/das/).</p>
<p><strong>Adding your own DAS Sources</strong></p>
<p>You can add your own DAS source to the list by clicking the
"Add Local Source" button. Enter the URL and nickname of your
<strong>0</strong> in order to attach it to the whole sequence.
Non-positional features are shown in a tooltip when the mouse
hovers over the sequence ID panel, and any embedded links can be
-accessed from the popup menu. <em>Scores</em><br>
+accessed from the popup menu.<br/> <em>Scores</em><br>
Scores can be associated with sequence features, and used to sort
sequences or shade the alignment (this was added in jalview 2.5).
The score field is optional, and malformed scores will be
features and groups on each sequence. To order the alignment using a
specific feature type, use the <em>sort by ..</em> entries in the pop-up
menu for that type.<br>
-<em>Feature sorting and graduated feature colouring was introduced
-in jalview 2.5</em></p>
+<em>Feature sorting and graduated feature colouring were introduced
+in Jalview 2.5</em></p>
<p><strong>Transparency and Feature Ordering</strong></p>
<p>It is important to realise that sequence features are often not
may be attached to one position along a stretch of sequence marked with
a secondary structure feature).</p>
<p>The ordering of the sequence features in the dialog box list is
-the order used by jalview for rendering sequence features. A feature at
+the order used by Jalview for rendering sequence features. A feature at
the bottom of the list is rendered <em>below</em> a feature higher up in
the list.<br>
<em><strong>You can change the order of a feature by
A more advanced hide involves a right-mouse click on a sequence, then
selecting <strong>"SequenceID -> Represent Group with
SequenceId"</strong>. Using this method of hiding sequences, any edits
-performed on the visible group representative will be propogated to all
+performed on the visible group representative will be propagated to all
the sequences in that group. <br>
The hidden representative sequences will not be used in any calculations
or web service alignments (<em>nb. this may change in the future</em>).
</head>
<body>
<p><strong>Multiple Alignment Views</strong></p>
-<p>Multiple alignment views allows the same alignment to be viewed
+<p>Multiple alignment views allow the same alignment to be viewed
independently in many different ways simultaneously. Each view is an
independent visualization of the same alignment, so each may have a
-different ordering, colouring, row and column hiding and seuqence
+different ordering, colouring, row and column hiding and sequence
feature and annotation display setting, but alignment, feature and
annotation edits are common to all, since this affects the underlying
data.</p>
<body>
<p><strong>Sequence Fetcher</strong></p>
<p>Jalview can retrieve sequences from certain databases using either the
-WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
+WSDBFetch service provided by the European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
<img src="seqfetcher.gif" align="center"
alt="The Jalview Sequence Fetcher Dialog Box">
<p>The Sequence Fetcher dialog box can be opened via the "File"
Structure:"</strong> option in
the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if
you can't see this, then no RNA structure is associated with your
-sequence or alignment. In the pop-up menu all structures that
+sequence or alignment). In the pop-up menu all structures that
are associated with this sequence and all sequences that are
associated with the alignment are available.
<b>Individual structures</b>:
this is a structure associated with the individual sequence and therefore not related to the alignment
</li>
-
+</ul>
<p><strong>Controls</strong><br>
<ul>
<li>Rotate view - Left Click and drag</li>
want an exact image of the alignment as displayed in Jalview. This is useful
if a 3rd Party EPS viewer does not have the same Font which the EPS file was
created with.</li>
-<li>When importing an EPS into to a Microsoft office document, a snapshot image of the
+<li>When importing an EPS file into a Microsoft office document, a snapshot image of the
file will be displayed which often looks blurred. Right-click the
image and choose "Edit image." to convert it to word
drawing objects which give a truer WYSIWIG representation.
</head>
<body>
-<p><strong>Alignment Fileformats</strong>
+<p><strong>Alignment File Formats</strong>
<p>Jalview understands a wide range of sequence alignment formats. In
order to determine which format has been used for an alignment,
jalview tries to detect some text or formatting unique to one of the formats:
Select the format of the text by selecting one of the following
menu items.</em>
<ul>
- <li><strong>FASTA</strong> <em></em>
- </li>
- <li><strong>MSF</strong>
- </li>
- <li><strong>CLUSTAL</strong>
- </li>
- <li><strong>BLC</strong>
- </li>
- <li><strong>PIR</strong>
- </li>
- <li><strong>PFAM</strong>
- </li>
+ <li><strong>FASTA</strong> </li>
+ <li><strong>MSF</strong></li>
+ <li><strong>CLUSTAL</strong></li>
+ <li><strong>BLC</strong></li>
+ <li><strong>PIR</strong></li>
+ <li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>Phylip</strong></li>
</ul></li>
<li><strong>Print (Control P)<br> </strong><em>Jalview
will print the alignment using the current fonts and colours of
the last redundancy deletion.</em>
</li>
<li><strong>Pad Gaps<br> </strong><em>When selected,
- the alignment will be kept at minimal width (so there no empty
+ the alignment will be kept at minimal width (so there are no empty
columns before or after the first or last aligned residue) and all
- sequences will be padded with gap characters to the before and
+ sequences will be padded with gap characters before and
after their terminating residues.<br> This switch is useful
when making a tree using unaligned sequences and when working with
alignment analysis programs which require 'properly aligned
undo the last redundancy deletion.</em></li>
<li><strong>Pad Gaps<br>
</strong><em>When selected, the alignment will be kept at minimal width (so
- there no empty columns before or after the first or last aligned
- residue) and all sequences will be padded with gap characters to the
+ there are no empty columns before or after the first or last aligned
+ residue) and all sequences will be padded with gap characters
before and after their terminating residues.<br>
This switch is useful when making a tree using unaligned sequences and
when working with alignment analysis programs which require 'properly
<li><strong>BLC</strong></li>
<li><strong>PIR</strong></li>
<li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>Phylip</strong></li>
</ul>
</li>
<li><strong>Page Setup ...</strong><br>
<body>
<p><strong>Privacy for Jalview Users</strong><br>
<p>The Jalview Desktop application which is available from the
-www.jalview.org site does not contain code designed collect personal or
+www.jalview.org site does not contain code designed to collect personal or
private information without your consent. However, we do collect usage
statistics to work out who is using Jalview, so we can apply for funding
to support Jalview development, and make it better for our users.</p>
</ul><br>
</li>
<li><em>Google Analytics</em><br>
- Since jalview 2.4.0b2, the Jalview Desktop records usage data with
+ Since Jalview 2.4.0b2, the Jalview Desktop records usage data with
Google Analytics via the <a
href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
class.<br>
href="features/commandline.html">command line options</a> to disable
the questionnaire and usage statistics check. Finally, the <a
href="features/preferences.html#connections">Connections Tab</a> of the
-jalview preferences contains options for controlling the submission of
+Jalview preferences contains options for controlling the submission of
usage statistics.
<p><strong>Other Web Clients in Jalview</strong><br>
The Jalview desktop is intended to make it easier to interact with
whilst it is still connected to a session, that session can be recovered
in a new Jalview instance using the <strong>Vamsas→"Existing
session"</strong> sub menu.</p>
-<strong>A quick Demo</strong>
+<p><strong>A quick Demo</strong>
<br>
Jalview can talk to itself through VAMSAS. Simply start two copies of
the application, create a new vamsas session in one, and connect to the
<em>Partition Function (-p)</em><br /> Calculate the Partition
Function and base pairing probability matrix in addition to the mfe
structure. A coarse representation of the pair probabilities in the
- from of a pseudo bracket notation, as well as the centroid structure
+ form of a pseudo bracket notation, as well as the centroid structure
derived from the pair probabilities are displayed. The most likely
base pairings are stored in a separate file by RNAalifold and
represented in Jalview by a bar graph annotation line labeled
<p><strong>The Sequence Identification Process</strong><br>
The method of accession id discovery is derived from the method which
earlier Jalview versions used for Uniprot sequence feature retrieval,
-and was originally restricted to the identifaction of valid Uniprot
+and was originally restricted to the identification of valid Uniprot
accessions.<br>
Essentially, Jalview will try to retrieve records from a subset of the databases
accessible by the <a href="../features/seqfetch.html">sequence
git://source.jalview.org / jalview.git / commitdiff