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.