X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=86acf934f559a49fa96de3bc1deb6cb6c630bba2;hb=2b3bd506ee1cc2d1a26a3425ccba48665179a9fb;hp=7584ca1fff019a2e74dfde33772392537e61257e;hpb=a14da63fa1dabed03c67eadc39c6b4a61c5102f0;p=jalview.git
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+++ b/help/html/menus/wsmenu.html
@@ -1,54 +1,81 @@
-
-Web Service Menu
-
-
-Web Service Menu
-
- 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.
-
- - Fetch DB References
- This will use the service WSDBFetch, provided by the EBI, to retrieve all
- database references and PDB ids associated with the selected sequences in
- the alignment if the sequences have valid Uniprot names or accession ids.
-
- - 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).
-
-
-
-
-
-
+
+
+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.
+
'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 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.
+
+ - 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. This enables you to align more 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).
+
+
+
+
+
+