X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=17e70ff0dee0f5abf8fe0b72031d379e6ed67744;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=7ee893b5c5f0f46dca3621a00753f6dd64755225;hpb=c554d41a4effc6719895bda6b3abc04c032715a8;p=jalview.git
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
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--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -1,56 +1,105 @@
-Web Service Menu
+
+
+Web Service Menu
+
-Web Service Menu
-
- - 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.
-
+
+ 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. DAS sequence servers and
+ the WSDBFetch service 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 plus any active DAS sequence sources<
+
Other submenus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+
- Selecting one of the following menu items starts a remote service
- on compute facilities at the University of Dundee. You need a continuous network
- connection in order to use these services through Jalview.
+ 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
-
- - ClustalW Multiple Sequence Alignment
- Submits all, or just the currently selected sequences for alignment
- with clustal W.
- - ClustalW Multiple Sequence Alignment Realign
- Submits the alignment or currently selected region for re-alignment
- with clustal W. Use this if you have added some new sequences to an existing
- alignment.
- - MAFFT Multiple Sequence Alignment
- Submits all, or just the currently selected region for alignment with
- MAFFT.
- - Muscle Multiple Protein Sequence Alignment
- Submits all, or just the currently selected sequences for alignment
- using Muscle. Do not use this if you are working with nucleic acid sequences.
-
-
- - Secondary Structure Prediction
-
- - JPred Secondary Structure Prediction
- Secondary structure prediction by network consensus. 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).
-
-
-
-
+ - 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.
+
+
+