2 <head><title>Web Services</title></head>
4 <p><strong>Web services</strong></p>
6 <p>Jalview includes clients for a variety of web services for both bioinformatic data retrieval and analysis.
8 <li>The <a href="../features/seqfetcher.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>
9 <li>The DAS Feature Fetcher enables the retrieval and visualization of features from DAS annotation sources</li>
10 <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>
11 Web Service</strong> menu.</li></ul>
13 <p>Jalview's distributed computations are SOAP based services exposing
14 protein sequence alignment and secondary structure prediction programs. These services actually run
15 on the cluster based in the School of Life Sciences, University of
16 Dundee, and are maintained by the Barton group.
18 <p><strong>Web Service Dialog Box</strong></p>
19 <img src="clwqueued.gif">
21 This dialog box is displayed when a web service job
22 is submitted. It gives the name of the service and
23 any method citation information, and monitors the
24 progress of the calculation. The cancel button will
25 permanently cancel the job, but this is only
26 possible for some services.
29 <ul><a href="msaclient.html"><strong>Multiple
30 Sequence Alignment Services</strong></a><ul>
31 <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>
32 The clustal W service remains one of the more
33 popular Jalview features.
35 <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
36 High Quality and High Throughput multiple alignments of proteins. This
37 method can sometimes be more accurate than ClustalW when dealing with
38 diverse sets of sequences.
40 <li><a href="mafft.html">MAFFT</a><br>
41 Multiple Alignment with Fast Fourier Transforms -
42 a highly accurate and high throughput dna and amino
43 acid alignment method, performing at least as well
44 as ClustalW and Muscle.
48 <li><strong>Secondary Structure Prediction</strong>
50 <li><a href="jnet.html">JNet</a><br>This is a front end to the existing <a
51 href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet
52 www server</a> allowing single sequence or profile
59 <p>Watch this space! These are some of the services
60 planned to be released soon:<ul>
63 <li>Remote Homology Detection<br>
66 In the future, Jalview will also be able to new discover services
67 dynamically, and distribute expensive analysis functions like <a
68 href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>