- <html>\r
- <head><title>Web Services</title></head>\r
- <body>\r
- <p><strong>Web services</strong></p>\r
- <p>A variety of web services are available from the Alignment window's\r
- <strong>Calculations→Web Service</strong> menu.\r
- </p>\r
- <p>Jalview's distributed computations are SOAP based services exposing\r
- protein sequence alignment and secondary structure prediction programs. These services actually run\r
- on the cluster based in the School of Life Sciences, University of\r
- Dundee, and are maintained by the Barton group.\r
- </p>\r
- <p><strong>Web Service Dialog Box</strong></p>\r
-<img src="clwqueued.gif">\r
-<p>\r
- This dialog box is displayed when a web service job\r
- is submitted. It gives the name of the service and\r
- any method citation information, and monitors the\r
- progress of the calculation. The cancel button will\r
- permanently cancel the job, but this is only\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
- </li>\r
- <li>Muscle Multiple Alignment<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
- <em>This is a front end to the existing JNet www server.</em>\r
- </li>\r
- </ul>\r
- </p>\r
- <p>Watch this space! These are some of the services\r
- planned to be released soon:<ul>\r
- <li>Repeat analysis\r
- </li>\r
- <li>Remote Homology Detection<br>\r
- </li>\r
- </ul>\r
- In the future, Jalview will also be able to new discover services\r
- dynamically, and distribute expensive analysis functions like <a\r
- href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>\r
-</body>\r
-</html>\r
+
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * 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>Jalview SOAP Web Services for sequence and alignment analysis
+ are provided by the University of Dundee, and are available from the
+ Alignment window's <strong> Web Service</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>Jalview 2.5 includes 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 members of <a
+ href="http://www.enfin.org">ENFIN</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>
+ </ul>
+ </li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <ul>
+ <li><a href="jnet.html">JNet</a><br>
+ This is a front end to the existing <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>
+<!-- <p>Watch this space! These are some of the services
+ planned to be released soon:<ul>
+ <li>More alignment services: PROBCONS, T-COFFEE</li>
+ <li>Repeat analysis
+ </li>
+ <li>Remote Homology Detection<br>
+ </li>
+ </ul>
+ In the future, Jalview will also be able to new discover services
+ dynamically, and distribute expensive analysis functions like <a
+ href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>-->
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff