X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=b8b357ed860bf07789eb8a584a6abbd8b7819977;hb=eb190489441b102c7dce1ee0121df7efd3e74b1a;hp=33282e9c70f86dfd9726a2513e62a851cdfc1be0;hpb=dde303bc73617ab4eb3e681e67cf899e6a971318;p=jalview.git
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index 33282e9..b8b357e 100755
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -29,14 +29,13 @@
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.
-
+ - 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:
@@ -45,7 +44,7 @@
in Jalview 2.8.1
- 'Standard Databases' will check sequences against the
- EBI databases plus any active DAS sequence sources<
+ EBI databases
Other submenus allow you to pick a specific source to query -
sources are listed alphabetically according to their nickname.
@@ -68,22 +67,22 @@
- JPred Secondary Structure Prediction
Secondary structure prediction by network consensus.
- See the Jpred3 client
+ 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 JNet prediction
+ 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 JNet prediction server for homolog detection
+ 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 Jnet prediction on the first
+ for a JPred prediction on the first
sequence in the set (that is, the one that appears first
in the alignment window).