X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=8f36013a24b75b1c439296ad334610ca467a5a53;hb=a3ca1aac6c00fc2240fa21be9df43adcc1b964ff;hp=021e31e4fa8703ba6f2041a6648edd308aeaaf9b;hpb=c24267ee9b42f032d0d1a561b6fb05b03d754460;p=jalview.git
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-
- 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.
-
- 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.
-
-
-
-
-
- Watch this space! These are some of the services
- planned to be released soon:
- - Repeat analysis
-
- - Remote Homology Detection
-
-
- In the future, Jalview will also be able to new discover services
- dynamically, and distribute expensive analysis functions like PCA to the Dundee machines.
+
+
+
+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 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.
+