X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=b41e643fc087df3fd313737a4f17c2c85ebe86f4;hb=a16c37a5983e3c581dc3d3030e1439e8fb3239f1;hp=815448bc61a096a3072b4f03d3d414aad66074a0;hpb=bccb0e877e424519b1d799278cdb529f974cb026;p=jalview.git
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+
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
+ Jalview includes clients for a variety of web services for both
+ bioinformatic data retrieval and analysis.
- - 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.
+ - 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
+ - The Database Reference
+ Fetcher transfers database references from records available from
+ DAS or 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).
-
- - Secondary Structure Prediction
-
- - JNet
- This is a front end to the existing JNet www server
- allowing single sequence or profile based prediction.
-
-
-
-
-
+
+
+ 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-performace Computing Cluster. With
+ the advent of JABAWS,
+ however, it is possible for anyone to host Jalview web services.
+
+
+ Envision2 Services
+
+
+
+ Since version 2.5, Jalview has included 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 ENFIN (www.enfin.org).
+