X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=25a5bef0054c74050bd697f1e02601cfe3083edc;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=2b24bfe4531938e0542a6992e0afc9e352b4cc62;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git
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-Web services
-Originally Jalview used SRS server to retrieve sequence features for a given
- alignment. In addition certain remote alignment programs could be called from
- the Jalview interface and the results displayed in a new alignment panel.
-The main emphasis of the current development of the Jalview Project is to implement
- various sequence alignment programs, tree analysis, PCA algorithms on a large
- cluster based witihin the Barton Group. Jalview will be able to call these remote
- procedures without the user having to install any new software.
- The main advantage of using these remote web services is that the computing
- power available is much greater than that of the users work station.
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+
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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
+ - 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:
+
+ - Jalview SOAP Web Services for sequence alignment and
+ secondary structure prediction based at the University of Dundee.
+ - Services for submitting IDs and sequences to external
+ bioinformatics services such as Envision2.
+ - Programs for multiple sequence alignment, made available via
+ Java Bioinformatic
+ Analysis Web Service (JABAWS) servers.
+
+ The Web Services Preference panel
+ controls the display and appearance of the submission and analysis
+ services in the Web Services 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
+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).
+
+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.
+ - Other alignment methods are also available via JABAWS. For more information about a
+ particular service, see the documentation available via the web services parameter dialog box.
+
+
+ - Secondary Structure Prediction
+
+ - JNet
+ This is a front end to the JNet www server
+ allowing single sequence or profile based prediction.
+
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+