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
uniprot database cross 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).