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.