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