X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=9245ec35adfe5969e12a47f6bf9b0aeb0eacc0a2;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=6b5c5e1397a53215a67ad6bc074d386bbee4929f;hpb=e3f4349374e532d0f9bb2bc163ff1783ca030fd6;p=jalview.git
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-
- Web Services
-
- Web services
-
-A variety of web services 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 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).
+
+
+
+ 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).
+
+
+