-<html>\r
-\r
-<body>\r
-<p><strong>Web services </strong></p>\r
-<p>Originally Jalview used SRS server to retrieve sequence features for a given \r
- alignment. In addition certain remote alignment programs could be called from \r
- the Jalview interface and the results displayed in a new alignment panel. </p>\r
-<p>The main emphasis of the current development of the Jalview Project is to implement \r
- various sequence alignment programs, tree analysis, PCA algorithms on a large \r
- cluster based witihin the Barton Group. Jalview will be able to call these remote \r
- procedures without the user having to install any new software. <br>\r
- The main advantage of using these remote web services is that the computing \r
- power available is much greater than that of the users work station.</p>\r
-</body>\r
-</html>\r
+
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<html>
+<head>
+<title>Web Services</title>
+</head>
+<body>
+<p><strong>Web services</strong></p>
+
+<p>Jalview includes clients for a variety of web services for both
+bioinformatic data retrieval and analysis.
+<ul>
+ <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
+ utilises web services for sequence, alignment and structure retrieval
+ provided by the European Bioinformatics Institute (EBI) and Distributed
+ Annotation System servers that are capable of serving sequences.</li>
+ <li>The <a href="../features/dasfeatures.html">DAS Feature
+ Fetcher</a> enables the retrieval and visualization of features from DAS
+ annotation sources</li>
+ <li>The <a href="dbreffetcher.html">Database Reference Fetcher</a>
+ transfers database references from records available from DAS or the
+ public sequence databases.</li>
+ <li>The <strong>Web Services</strong> menu in each alignment
+ window also provides access to the following:
+ <ul>
+ <li>Jalview SOAP Web Services for sequence alignment and
+ secondary structure prediction based at the University of Dundee.</li>
+ <li>Services for submitting IDs and sequences to external
+ bioinformatics services such as <a href="#envision2">Envision2</a>.</li>
+ <li>Programs for multiple sequence alignment, made available <em>via</em>
+ <a href="JABAWS.html">Java Bioinformatic
+ Analysis Web Service (JABAWS)</a> servers.</li>
+ </ul>
+ The <a href="webServicesPrefs.html">Web Services Preference panel</a>
+ controls the display and appearance of the submission and analysis
+ services in the <strong>Web Services</strong> menu.</li>
+
+</ul>
+</p>
+<p>Jalview's distributed computations are SOAP based services
+exposing protein sequence alignment and secondary structure prediction
+programs. These services actually run on the cluster based in the School
+of Life Sciences, University of Dundee, and are maintained by the Barton
+group.</p>
+<p><strong><a name="envision2">Envision2 Services</a></strong></p>
+<p>Since version 2.5, Jalview has included a client to enable the
+user to submit one or more sequences or sequence IDs to analysis
+workflows provided by the <a
+ href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
+application</a>. This allows Jalview users to easily access the EnCore
+network of databases and analysis services developed by ENFIN (<a
+ href="http://www.enfin.org">www.enfin.org</a>).</p>
+<br />
+<p><strong>Web Service Dialog Box</strong></p>
+<img src="clwqueued.gif">
+<p>This dialog box is displayed when a web service job is submitted.
+It gives the name of the service and any method citation information,
+and monitors the progress of the calculation. The cancel button will
+permanently cancel the job, but this is only possible for some services.
+</p>
+<p>Current services:
+<ul>
+ <a href="msaclient.html"><strong>Multiple Sequence
+ Alignment Services</strong></a>
+ <ul>
+ <li><a href="clustalw.html">ClustalW Multiple Alignment and
+ re-alignment</a><br>
+ The clustal W service remains one of the more popular Jalview
+ features.</li>
+ <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
+ High Quality and High Throughput multiple alignments of proteins. This
+ method can sometimes be more accurate than ClustalW when dealing with
+ diverse sets of sequences.</li>
+ <li><a href="mafft.html">MAFFT</a><br>
+ Multiple Alignment with Fast Fourier Transforms - a highly accurate
+ and high throughput dna and amino acid alignment method, performing at
+ least as well as ClustalW and Muscle.</li>
+ <li>Other alignment methods are also available via <a
+ href="JABAWS.html">JABAWS</a>. For more information about a
+ particular service, see the documentation available via the <a
+ href="webServicesParams.html">web services parameter dialog box</a>.</li>
+ </ul>
+ </li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <ul>
+ <li><a href="jnet.html">JNet</a><br>
+ This is a front end to the <a
+ href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet www server</a>
+ allowing single sequence or profile based prediction.</li>
+ </ul>
+ </li>
+</ul>
+</p>
+
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff