#-------------------------------------------------------------------------------
# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
#
# This file is part of Jalview.
#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see .
#-------------------------------------------------------------------------------
Web Service Menu
Web Service Menu
- Fetch DB References
This will use 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 the sequence and retrieve all database cross references and PDB ids
associated with all or just the selected sequences in the alignment.
'Standard Databases' will check sequences against the EBI databases
plus any active DAS sequence sources, or you can verify against a specific
source from one of the sub-menus.
- Envision2 Services
Submits one or more sequences, sequence IDs or database references to analysis workflows provided
by the EnVision2
web application. This allows Jalview users to easily access the EnCore network of
databases and analysis services developed by members of ENFIN.
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. This enables you to align more 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).