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+Web Service Menu
+
+
+ Web Service Menu
This menu
+ is dynamic, and may contain user-defined web service entries in
+ addition to any of the following ones:
+
+ - Fetch DB References
This
+ will use any of the database services that Jalview is aware of
+ (e.g. DAS sequence servers and the WSDBFetch service provided by
+ the EBI) to verify the sequence and retrieve all database cross
+ references and PDB ids associated with all or just the selected
+ sequences in the alignment.
'Standard Databases' will check
+ sequences against the EBI databases plus any active DAS sequence
+ sources, or you can verify against a specific source from one of
+ the sub-menus.
+ - Envision2 Services
Submits one or
+ more sequences, sequence IDs or database references 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.
+
+ Selecting items from the following submenus will start a
+ remote service on compute facilities at the University of Dundee, or
+ elsewhere. You need a continuous network connection in order to use
+ these services through Jalview.
+
+
+ - Alignment
Align the currently
+ selected sequences or all sequences in the alignment, or re-align
+ unaligned sequences to the aligned sequences. Entries in this menu
+ provide access to the various alignment programs supported by JABAWS. See the Multiple Sequence
+ Alignment webservice client entry for more information.
+ - Secondary Structure Prediction
+
+ - JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. See
+ the Jpred3 client entry for
+ more information. The behaviour of this calculation depends on
+ the current selection:
+
+ - If nothing is selected, and the displayed sequences
+ appear to be aligned, then a JNet prediction will be run for
+ the first sequence in the alignment, using the current
+ alignment. Otherwise the first sequence will be submitted for
+ prediction.
+ - If just one sequence (or a region on one sequence) has
+ been selected, it will be submitted to the automatic JNet
+ prediction server for homolog detection and prediction.
+ - If a set of sequences are selected, and they appear to
+ be aligned, then the alignment will be used for a Jnet
+ prediction on the first sequence in the set
+ (that is, the one that appears first in the alignment window).
+
+
+
+ - Analysis
+
+ - Sequence Harmony Multi-Relief
Performs
+ functional residue analysis on a protein family alignment with
+ sub-families defined on it. See the SHMR client entry for more
+ information.
+
+
+
+
+