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.

• 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.
  • Muscle Multiple Protein Sequence Alignment
    Submits all, or jut 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).