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-
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Web Services
-Web services
+
+ Web services
+
-Jalview includes clients for a variety of web services for both
-bioinformatic data retrieval and analysis.
-
- - The Sequence Fetcher
- 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.
- - The DAS Feature Fetcher enables the retrieval and
- visualization of features from DAS annotation sources
- - Jalview SOAP Web Services for sequence and alignment analysis
- are provided by the University of Dundee, and are available from the
- Alignment window's Web Service menu.
-
-
-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.
-Envision2 Services
-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 EnVision2
-web application. This allows Jalview users to easily access the EnCore network of
-databases and analysis services developed by members of ENFIN.
-
-Web Service Dialog Box
-
-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.
-
-Current services:
-
- Multiple Sequence
- Alignment Services
-
- - ClustalW Multiple Alignment and
- re-alignment
- The clustal W service remains one of the more popular Jalview
- features.
- - Muscle Multiple Alignment
- 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.
- - MAFFT
- 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.
-
-
- - Secondary Structure Prediction
-
- - JNet
- This is a front end to the existing JNet www server
- allowing single sequence or profile based prediction.
-
-
-
-
-
+ Jalview includes clients for a variety of web services for both
+ bioinformatic data retrieval and analysis.
+
+ - The Sequence
+ Fetcher 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.
+
+ - The Database Reference
+ Fetcher transfers database references and annotation from the public
+ sequence databases.
+
+ - The Web Services menu in each alignment
+ window also provides access to the following:
+
+
+ Web Service Dialog Box
+
+ 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.
The Web Services Preference
+ panel controls the display and appearance of the submission and
+ analysis services in the Web Services menu.
+
+ - If Jalview encounters problems accessing any services, it
+ may display a warning
+ dialog box (this can be turned off using the web services
+ preferences tab).
+
+
+
+
+ More about Jalview's Web Services
+ Jalview's distributed computations utilise SOAP and REST
+ web services exposing sequence alignment, analysis, and secondary
+ structure prediction programs. Originally, Jalview 2's services were
+ maintained by the Barton group at the University of Dundee, and ran
+ programs on the Life Sciences High-performance Computing Cluster.
+ With the advent of JABAWS,
+ however, it is possible for anyone to host Jalview web services.
+