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2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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19 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
20 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
22 * This file is part of Jalview.
24 * Jalview is free software: you can redistribute it and/or
25 * modify it under the terms of the GNU General Public License
26 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
28 * Jalview is distributed in the hope that it will be useful, but
29 * WITHOUT ANY WARRANTY; without even the implied warranty
30 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
31 * PURPOSE. See the GNU General Public License for more details.
33 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
37 <title>Web Services</title>
40 <p><strong>Web services</strong></p>
42 <p>Jalview includes clients for a variety of web services for both
43 bioinformatic data retrieval and analysis.
45 <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
46 utilises web services for sequence, alignment and structure retrieval
47 provided by the European Bioinformatics Institute (EBI) and Distributed
48 Annotation System servers that are capable of serving sequences.</li>
49 <li>The <a href="../features/dasfeatures.html">DAS Feature
50 Fetcher</a> enables the retrieval and visualization of features from DAS
51 annotation sources</li>
52 <li>The <a href="dbreffetcher.html">Database Reference Fetcher</a>
53 transfers database references from records available from DAS or the
54 public sequence databases.</li>
55 <li>Jalview SOAP Web Services for sequence and alignment analysis
56 are provided by the University of Dundee, and are available from the
57 Alignment window's <strong> Web Service</strong> menu.</li>
60 <p>Jalview's distributed computations are SOAP based services
61 exposing protein sequence alignment and secondary structure prediction
62 programs. These services actually run on the cluster based in the School
63 of Life Sciences, University of Dundee, and are maintained by the Barton
65 <p><strong><a name="envision2">Envision2 Services</a></strong></p>
66 <p>Jalview 2.5 includes a client to enable the user to submit one or
67 more sequences or sequence IDs to analysis workflows provided by the <a
68 href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
69 application</a>. This allows Jalview users to easily access the EnCore
70 network of databases and analysis services developed by members of <a
71 href="http://www.enfin.org">ENFIN</a>.</p>
73 <p><strong>Web Service Dialog Box</strong></p>
74 <img src="clwqueued.gif">
75 <p>This dialog box is displayed when a web service job is submitted.
76 It gives the name of the service and any method citation information,
77 and monitors the progress of the calculation. The cancel button will
78 permanently cancel the job, but this is only possible for some services.
82 <a href="msaclient.html"><strong>Multiple Sequence
83 Alignment Services</strong></a>
85 <li><a href="clustalw.html">ClustalW Multiple Alignment and
87 The clustal W service remains one of the more popular Jalview
89 <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
90 High Quality and High Throughput multiple alignments of proteins. This
91 method can sometimes be more accurate than ClustalW when dealing with
92 diverse sets of sequences.</li>
93 <li><a href="mafft.html">MAFFT</a><br>
94 Multiple Alignment with Fast Fourier Transforms - a highly accurate
95 and high throughput dna and amino acid alignment method, performing at
96 least as well as ClustalW and Muscle.</li>
99 <li><strong>Secondary Structure Prediction</strong>
101 <li><a href="jnet.html">JNet</a><br>
102 This is a front end to the existing <a
103 href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet www server</a>
104 allowing single sequence or profile based prediction.</li>
109 <!-- <p>Watch this space! These are some of the services
110 planned to be released soon:<ul>
111 <li>More alignment services: PROBCONS, T-COFFEE</li>
114 <li>Remote Homology Detection<br>
117 In the future, Jalview will also be able to new discover services
118 dynamically, and distribute expensive analysis functions like <a
119 href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>-->