- <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.
+
+<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/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>
-<li>The DAS Feature Fetcher enables the retrieval and visualization of features from DAS annotation sources</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>
+ <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>
+ <li>The DAS Feature Fetcher enables the retrieval and
+ visualization of features from DAS annotation sources</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>Web Service Dialog Box</strong></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
+<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>
</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>
+ href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>-->
</body>
</html>
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