<mapID target="cursor" url="html/features/cursorMode.html"/>\r
<mapID target="search" url="html/features/search.html"/> \r
<mapID target="webservice" url="html/webServices/index.html"/>\r
+ <mapID target="msaservice" url="html/webServices/msaclient.html"/>\r
<mapID target="clustal" url="html/webServices/clustalw.html"/>\r
<mapID target="muscle" url="html/webServices/muscle.html"/>\r
<mapID target="mafft" url="html/webServices/mafft.html"/>\r
<mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
<mapID target="redundancy" url="html/calculations/redundancy.html"/>\r
<mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>\r
- \r
+ <mapID target="recoverInputdata" url="html/calculations/recoverInputdata.html"/>\r
<mapID target="colours" url="html/colourSchemes/index.html" />\r
<mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>\r
<mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />\r
<toc version="1.0">\r
<tocitem text="Jalview Documentation" target="home" expand="true" >\r
<tocitem text="What's new" target="new" expand="false">\r
- <tocitem text="MAFFT Alignment" target="mafft"/>\r
<tocitem text="DAS Feature Fetching" target="das.settings"/>\r
- <tocitem text="Hide Regions" target="hiddenRegions"/> \r
+ <tocitem text="Hide Regions" target="hiddenRegions"/>\r
+ <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>\r
+ <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>\r
+ <tocitem text="MAFFT Alignment" target="mafft"/>\r
</tocitem>\r
<tocitem text="Release History" target="release"/>\r
<tocitem text="Editing Alignments" target ="edit"/> \r
<tocitem text="DAS Features Settings" target="das.viewing"/>\r
</tocitem>\r
<tocitem text="Web Services" target="webservice" expand="false">\r
+ <tocitem text="Sequence Alignment" target="msaservice" expand="false">\r
<tocitem text="Clustal Alignment" target="clustal"/>\r
<tocitem text="Muscle Alignment" target="muscle"/>\r
<tocitem text="MAFFT Alignment" target="mafft"/>\r
- <tocitem text="JNet Prediction" target="jnet"/>\r
+ </tocitem>\r
+ <tocitem text="Secondary Structure Prediction" target="jnet"/>\r
</tocitem>\r
<tocitem text="Colour Schemes" target="colours" expand="false">\r
<tocitem text="ClustalX" target="colours.clustal"/>\r
--- /dev/null
+<html>\r
+<head><title>Viewing Input Data to PCA and Tree calculations</title></head>\r
+<body>\r
+\r
+<p><strong>Viewing Input Data to PCA and Tree calculations</strong></p>\r
+<p>It is always possible to retrieve the input data used to calculate\r
+ a tree or PCA plot by using the analysis window's \r
+ <strong>"File \r
+ -> Input Data..."</strong> menu item. The Input Data will be\r
+ shown in a new alignment window, with any hidden columns\r
+ preserved.</p>\r
+</body>\r
+</html>\r
\r
<body>\r
<p><strong>DAS Settings</strong></p>\r
-<p>Jalview can retrieve features from multiple <a href="http://biodas.org/">DAS</a> \r
- sources. The DAS sources are selected in the DAS settings panel.</p>\r
+<p>Jalview can retrieve and visualize features from many <a href="http://biodas.org/">DAS</a> \r
+ sources at once. The DAS sources are discovered and selected <em>via</em> the DAS settings panel.</p>\r
<p><img src="das.jpg" width="497" height="365">\r
-<p>On start up of the DAS Settings panel, Jalview will use the registry URL (default \r
- is http://das.sanger.ac.uk/registry/das1/sources/) to retrieve a list of currently \r
- available DAS sources. These are all listed in the table using the sources' \r
- Nickname as an identifier. <br>\r
- Click on a Nickname in the table to reveal more information about that service \r
- in the panel to the right of the table. \r
+<p>The available sources are listed in the table using each source's\r
+Nickname as its identifier. Clicking on a source's entry in the table\r
+reveals more information about that service in the panel to the\r
+right. Select the tickbox in the "Use Source" column for a\r
+source to add it to the set Jalview queries for alignment and sequence\r
+features.\r
+</p>\r
<p>You can filter the visible DAS sources by authority, type and "label". \r
You should read the DAS documentation to understand more about these values.\r
-<p>Tick the box "Use Source" so that Jalview will use a particular source \r
- when fetching features. \r
+<p><strong>Updating the list of sources</strong></p>\r
+<p>When the DAS Settings panel is first opened, and when the <strong>'Refresh\r
+ source'</strong> buton is pressed, a list of DAS sources\r
+ is retrieved from the DAS registry URL (set by default to the DAS\r
+ registration server at\r
+ http://das.sanger.ac.uk/registry/das1/sources/).</p>\r
+<p><strong>Adding your own DAS Sources</strong></p>\r
<p>You can add your own DAS source to the list by clicking the "Add Local \r
Source" button. Enter the URL and nickname of your additional service. \r
It should be noted that Jalview 2.1 will not query additional sources for more \r
<p>Use the keyboard key "H" to hide / reveal selected columns and sequences. \r
To hide / reveal only selected sequences, use "Shift H", to hide / \r
reveal only selected columns, use "Control H".</p>\r
-<p> </p>\r
-<p>To <strong>hide selected sequences </strong>from an alignment, use the "View \r
- -> Hide -> Selected Sequences" menu item or simply select "Hide \r
- Sequences" from the Popup menu after a right click on the sequence Ids. \r
+<p><strong><em>Hiding Sequences</em></strong><br>\r
+To hide selected sequences in an alignment, use the <strong>"View \r
+ -> Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide \r
+ Sequences"</strong> from the Popup menu after a right click on the sequence Ids. \r
</p>\r
<p>Hidden sequences will not be used in any calculations, editing or web service \r
alignments performed on visible sequences. </p>\r
-<p>A more advanced hide involves a right-mouse click on a sequence, then selecting \r
- "SequenceID -> Represent Group with SequenceId". Using this method \r
+<p><strong><em>Hidden Sequences Representatives</em></strong><br>\r
+A more advanced hide involves a right-mouse click on a sequence, then selecting \r
+ <strong>"SequenceID -> Represent Group with SequenceId"</strong>. Using this method \r
of hiding sequences, any edits performed on the visible group representative \r
will be propogated to all the sequences in that group. <br>\r
- The hidden sequences will not be used in any calculations or web service alignments. \r
+ The hidden representative sequences will not be used in any\r
+ calculations or web service alignments (<em>nb. this may change in\r
+ the future</em>)\r
</p>\r
-<p> </p>\r
-<p>To <strong>hide selected columns</strong> from an alignment, use the "View \r
- -> Hide -> Selected Columns" menu item, or right click within a region \r
+<p><strong><em>Hiding Columns</em></strong><br>\r
+To hide selected columns in an alignment, use the <strong>"View \r
+ -> Hide -> Selected Columns"</strong> menu item, or right click within a region \r
of selected columns in the scale above the alignment (only available in non \r
- wrapped mode) and select "Hide Columns". </p>\r
-<p>Hidden columns will not be used in any calculations. This allows you to eg. \r
- create trees from the visible alignment and ignore any poorly aligned sections \r
- of the alignment, without cutting and deleting them permanently from your alignment.<br>\r
- It is possible to retrieve the input data to any trees, PCA analysis windows \r
- which were created from alignments containing hidden columns by using the "File \r
- -> Input Data..." menu item from the tree window. </p>\r
-<p> Editing the alignment is bound by the hidden columns, ie you cannot move residues \r
- across a hidden column boundary.</p>\r
-<p>Any web service alignments performed on sequences which contain hidden columns \r
- send the alignment as a series of chunks delimited by the hidden columns. </p>\r
+ wrapped mode) and select <strong>"Hide Columns"</strong>. </p>\r
+<p>When an alignment view contains hidden columns, certain constraints\r
+apply:<ul><li>Editing the alignment is bound by the hidden columns, <em>i.e.</em> you cannot move residues \r
+ across a hidden column boundary.</li>\r
+<li><strong>Tree</strong>, <strong>pairwise alignment</strong> and <strong>PCA</strong> calculations will only be\r
+performed using the <em>visible</em> parts of the alignment.\r
+</li>\r
+<li><a\r
+ href="../webservices/msaclient.html">Multiple Sequence\r
+ Alignments</a> are performed locally on on each visible chunk of\r
+ the input, and concatenated with the hidden regions to form the\r
+ final result.</p>\r
+</li>\r
+</ul>\r
+<p>The analysis and web service calculations where hidden columns are\r
+ excluded are termed <em>column-separable</em>. Calculations which\r
+ are not column-separable will be performed on the whole alignmnent\r
+ or sequence set, not just the visible regions.</p>\r
<p> </p>\r
<p> </p>\r
<p> </p>\r
possible for some services.\r
</p>\r
<p>Current services:\r
- <ul>\r
- <li>ClustalW Multiple Alignment<br>\r
- The clustal W service remains one of the more popular Jalview features.\r
+ <ul><a href="msaclient.html"><strong>Multiple\r
+ Sequence Alignment Services</strong></a><ul>\r
+ <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>\r
+ The clustal W service remains one of the more\r
+ popular Jalview features.\r
</li>\r
- <li>Muscle Multiple Alignment<br>\r
+ <li><a href="muscle.html">Muscle Multiple Alignment</a><br>\r
High Quality and High Throughput multiple alignments of proteins. This\r
method can sometimes be more accurate than ClustalW when dealing with\r
diverse sets of sequences.\r
</li>\r
- <li>JNet Secondary Structure Prediction<br>\r
- This is a front end to the existing JNet www server.\r
+ <li><a href="mafft.html">MAFFT</a><br>\r
+ Multiple Alignment with Fast Fourier Transforms -\r
+ a highly accurate and high throughput dna and amino\r
+ acid alignment method, performing at least as well\r
+ as ClustalW and Muscle.\r
+ </li>\r
+ </ul> \r
+ </li>\r
+ <li><strong>Secondary Structure Prediction</strong>\r
+ <ul>\r
+ <li><a href="jnet.html">JNet</a><br>This is a front end to the existing <a\r
+ href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet\r
+ www server</a> allowing single sequence or profile\r
+ based prediction.\r
+ </li>\r
+ </ul>\r
</li>\r
</ul>\r
</p>\r
nearest the top of the alignment window).\r
</li>\r
</ul>\r
+<p><strong>Note</strong>: JNet secondary structure prediction is a\r
+ 'non-column-separable' service - predictions are based on the\r
+ sequence profile of contiguous stretches of amino-acid sequence. This\r
+ means that all columns of the alignment, or selection will be submitted\r
+ for prediction, not just the visible ones (see <a\r
+ href="../features/hiddenRegions.html">hiding columns</a>).\r
<p>The result of a JNet prediction for a sequence is a new annotated\r
alignment window:</p>\r
<img src="jnetprediction.gif">\r
<html>\r
-<head><title>MAFFT Alignment</title></head>\r
+<head><title>MAFFT Multiple Sequence Alignments</title></head>\r
<body>\r
-<p><strong>MAFFT Alignments</strong></p>\r
-<p>MAFFT is a program for the alignment of many protein sequences.</p>\r
+<p><strong>MAFFT Multiple Sequence Alignments</strong></p>\r
<p> Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "MAFFT version \r
5: improvement in accuracy of multiple sequence alignment." Nucleic Acids \r
Research, 33 511-518</p>\r
-<p> This alignment method is applied to the selected region, if any, or the whole \r
- sequence set when the <strong>Web Service→Alignment→MAFFT Multiple \r
- Sequence Alignment</strong> menu item is selected. </p>\r
+<p>MAFFT is a program for the multiple alignment of nucleic acid or protein\r
+sequences, and is available from the <strong>Web\r
+Service→Alignment→MAFFT Multiple Sequence\r
+Alignment</strong> entry in the web services menu.</p>\r
+<p>MAFFT utilizes algorithms for spectral correlation to identify\r
+homologous regions in a fast-fourier transform representation of each\r
+sequence. The Jalview web service runs MAFFT using the\r
+'--auto' option which picks optimal parameters\r
+for the set of sequences to be aligned.</p>\r
</body>\r
</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<title>Multiple Sequence Alignment Web Service</title>\r
+</head>\r
+<body>\r
+<strong>Multiple Sequence Alignment Web Services</strong>\r
+<p>\r
+Multiple sequence alignment services are accessed from the <strong>Web\r
+Service→Alignment</strong> menu. When an entry from this menu is\r
+selected, either the currently selected residues, or the whole\r
+sequence set (if there is no selection or only one sequence is\r
+selected) will be submitted for multiple sequence alignment.\r
+</p>\r
+<p>There are two kinds of multiple sequence alignment operations\r
+available:<ul>\r
+<li><em>alignment</em> - where a new alignment is constructed from the input\r
+</li>\r
+<li><em>realignment</em> -\r
+where any existing alignments in the input are passed to the service\r
+for profile based alignment.\r
+</li>\r
+</ul>\r
+</p>\r
+<p>\r
+<strong>Multiple Alignments of Sequences with hidden columns</strong><br>\r
+Multiple alignment services are 'column separable' analysis\r
+operations. If the input contains <a\r
+href="../features/hiddenRegions.html">hidden columns</a> then each\r
+visible segment of the input sequence set will be submitted for\r
+alignment separately, and the results concatenated (with the hidden\r
+regions preserved) once all alignment functions have completed. Each\r
+sub-job's state is reported in its own tab:\r
+<p><center><strong>Multiple Multiple Sequence Alignment sub jobs running at\r
+once</strong><center></p>\r
+<center><img src="multimafftjbs.gif" align="centre"></center>\r
+</p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff
