X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=b8b357ed860bf07789eb8a584a6abbd8b7819977;hb=54cbe6eeaf683e042246c657716514d80e561a9c;hp=7584ca1fff019a2e74dfde33772392537e61257e;hpb=a14da63fa1dabed03c67eadc39c6b4a61c5102f0;p=jalview.git
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-
-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
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 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:
+ 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
+
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.
+
+
+
+
+