X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=b8b357ed860bf07789eb8a584a6abbd8b7819977;hb=eb190489441b102c7dce1ee0121df7efd3e74b1a;hp=f3a4102df19fd2e42e6a4396adf05f14222410ae;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
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@@ -1,84 +1,103 @@
-Web Service Menu
+ -->
+
+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.
-
- 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
-
- - Multi-Harmony
Performs
- functional residue analysis on a protein family alignment with
- sub-families defined on it. See the Multi-Harmony service entry for more
- information.
-
-
-
+
+ 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 submenu
+ contains options for accessing any of the database services that
+ Jalview is aware of (e.g services provided by the EBI) to verify
+ sequence start/end positions and retrieve all database cross
+ references and PDB ids associated with all or just the selected
+ sequences in the alignment.
+
+ - 'Retrieve full Sequence' - when checked, Jalview will
+ retrieve the full sequence for any accessions associated
+ with sequences in the alignment.
Note:
+ This could cause out of memory errors when working with
+ genomic sequence records !
Added
+ in Jalview 2.8.1
+
+ - 'Standard Databases' will check sequences against the
+ EBI databases
+
Other submenus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+
+
+ 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 Jpred 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 JPred 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 JPred 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 JPred prediction on the first
+ sequence in the set (that is, the one that appears first
+ in the alignment window).
+
+
+
+
+ - Analysis
+
+ - Multi-Harmony
Performs
+ functional residue analysis on a protein family alignment
+ with sub-families defined on it. See the Multi-Harmony
+ service entry for more information.
+
+
+