X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=0e050b1c1dd6c45dcf52ee731f2dbcc90be307b5;hb=7fd07d9b6a64aa33e3dcab2fa2f8bc20be189f2f;hp=8c85b934ca6a2bec6d025cf3fadaf87e19d4d7ce;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
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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).
-
-
-
-
+ 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 Jpred3 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 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).
+
+
+
+ - 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.
+
+
+