Web Service Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=b71bc1a07384065c8750cd4bc566e53fc8983dcc;hb=88fc5c47739a041ccd17053f8b390ed4bba831b1;hp=9dbfe8136f5a9df38deb7b57c59ecc1f86b6d142;hpb=d46f2f52b52c1495b92707ab6ad520bb1e465d5e;p=jalview.git diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index 9dbfe81..b71bc1a 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -1,49 +1,104 @@ - -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.

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
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 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. +

+ +