3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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/seqfetch.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 <a href="../features/dasfeatures.html">DAS Feature
34 Fetcher</a> enables the retrieval and visualization of features from DAS
35 annotation sources</li>
36 <li>The <a href="dbreffetcher.html">Database Reference Fetcher</a>
37 transfers database references from records available from DAS or the
38 public sequence databases.</li>
39 <li>The <strong>Web Services</strong> menu in each alignment
40 window also provides access to the following:
42 <li>Jalview SOAP Web Services for sequence alignment and
43 secondary structure prediction based at the University of Dundee.</li>
44 <li>Services for submitting IDs and sequences to external
45 bioinformatics services such as <a href="#envision2">Envision2</a>.</li>
46 <li>Programs for multiple sequence alignment, made available <em>via</em>
47 <a href="JABAWS.html">Java Bioinformatic Analysis Web Service
48 (JABAWS)</a> servers.</li>
50 The <a href="webServicesPrefs.html">Web Services Preference panel</a>
51 controls the display and appearance of the submission and analysis
52 services in the <strong>Web Services</strong> menu.</li>
53 <li>If Jalview encounters problems accessing any services, it may
54 display a <a href="webServicesPrefs.html#wswarnings">warning dialog
55 box</a> (this can be turned off using the web services preferences tab).</li>
58 <p><strong>More about Jalview's Web Services</strong> <br>
59 Jalview's distributed computations are SOAP based services exposing
60 protein sequence alignment and secondary structure prediction programs.
61 These services actually run on the cluster based in the School of Life
62 Sciences, University of Dundee, and are maintained by the Barton group.</p>
63 <p><strong><a name="envision2">Envision2 Services</a></strong></p>
64 <p>Since version 2.5, Jalview has included a client to enable the
65 user to submit one or more sequences or sequence IDs to analysis
66 workflows provided by the <a
67 href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
68 application</a>. This allows Jalview users to easily access the EnCore
69 network of databases and analysis services developed by ENFIN (<a
70 href="http://www.enfin.org">www.enfin.org</a>).</p>
72 <p><strong>Web Service Dialog Box</strong></p>
73 <img src="clwqueued.gif">
74 <p>This dialog box is displayed when a web service job is submitted.
75 It gives the name of the service and any method citation information,
76 and monitors the progress of the calculation. The cancel button will
77 permanently cancel the job, but this is only possible for some services.
81 <a href="msaclient.html"><strong>Multiple Sequence
82 Alignment Services</strong></a>
84 <li><a href="clustalw.html">ClustalW Multiple Alignment and
86 The clustal W service remains one of the more popular Jalview
88 <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
89 High Quality and High Throughput multiple alignments of proteins. This
90 method can sometimes be more accurate than ClustalW when dealing with
91 diverse sets of sequences.</li>
92 <li><a href="mafft.html">MAFFT</a><br>
93 Multiple Alignment with Fast Fourier Transforms - a highly accurate
94 and high throughput dna and amino acid alignment method, performing at
95 least as well as ClustalW and Muscle.</li>
96 <li>Other alignment methods are also available via <a
97 href="JABAWS.html">JABAWS</a>. For more information about a
98 particular service, see the documentation available via the <a
99 href="webServicesParams.html">web services parameter dialog box</a>.</li>
102 <li><strong>Secondary Structure Prediction</strong>
104 <li><a href="jnet.html">JNet</a><br>
105 This is a front end to the <a
106 href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet www server</a>
107 allowing single sequence or profile based prediction.</li>