X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=b8b357ed860bf07789eb8a584a6abbd8b7819977;hb=a510e9b4726214441e4fdac8a1d6752263c4c73d;hp=ee44c91952a4924b0fb076cb6411cfddd9402b62;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index ee44c91..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.
@@ -55,13 +54,12 @@
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
+ - 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.
@@ -69,22 +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).
@@ -96,8 +94,8 @@
- 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.
+ href="../webServices/shmr.html">Multi-Harmony
+ service
entry for more information.