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* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
---!>
-Web Service Menu
-
-
-Web Service Menu
-
- - Fetch DB References
- This will use 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 the sequence and retrieve all database cross references and PDB ids
- associated with all or just the selected sequences in the alignment.
-
'Standard Databases' will check sequences against the EBI databases
- plus any active DAS sequence sources, or you can verify against a specific
- source from one of the sub-menus.
-
- - Envision2 Services
- Submits one or more sequences, sequence IDs or database references to analysis workflows provided
-by the EnVision2
-web application. This allows Jalview users to easily access the EnCore network of
-databases and analysis services developed by members of ENFIN.
-
-
- 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. This enables you to align more 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).
-
-
-
-
-
-