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. those provided by
EMBL-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.
- 'Trim Retrieved Sequences' - when checked, Jalview will
discard any additional sequence data for accessions associated
with sequences in the alignment.
Note:
Disabling 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 sub-menus 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).
- Protein Disorder Prediction
Allows access to a range of protein disorder predictors
provided by JABAWS 2.2.
- 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.