Web Service Menu

From: jprocter Date: Tue, 8 May 2007 16:53:56 +0000 (+0000) Subject: formatting and wording X-Git-Tag: Release_2_3~21 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=89fcbb9f03f1a8b29509beb2588fd320f804d1fd;p=jalview.git formatting and wording --- diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index 7584ca1..a1df34a 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -1,54 +1,54 @@ - -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

+ 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 + uniprot database cross 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).
+

+ +