X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=021e31e4fa8703ba6f2041a6648edd308aeaaf9b;hb=4de388d1d73eb67fe9ccbfeb5f3483a0fe3052e8;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
+- 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.
+
+