#-------------------------------------------------------------------------------
# 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 Services
Web services
Jalview includes clients for a variety of web services for both
bioinformatic data retrieval and analysis.
- The Sequence Fetcher
utilises web services for sequence, alignment and structure retrieval
provided by the European Bioinformatics Institute (EBI) and Distributed
Annotation System servers that are capable of serving sequences.
- The DAS Feature
Fetcher enables the retrieval and visualization of features from DAS
annotation sources
- The Database Reference Fetcher
transfers database references from records available from DAS or the
public sequence databases.
- Jalview SOAP Web Services for sequence and alignment analysis
are provided by the University of Dundee, and are available from the
Alignment window's Web Service menu.
Jalview's distributed computations are SOAP based services
exposing protein sequence alignment and secondary structure prediction
programs. These services actually run on the cluster based in the School
of Life Sciences, University of Dundee, and are maintained by the Barton
group.
Envision2 Services
Jalview 2.5 includes a client to enable the user to submit one or
more sequences or sequence IDs 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.
Web Service Dialog Box
This dialog box is displayed when a web service job is submitted.
It gives the name of the service and any method citation information,
and monitors the progress of the calculation. The cancel button will
permanently cancel the job, but this is only possible for some services.
Current services:
Multiple Sequence
Alignment Services
- ClustalW Multiple Alignment and
re-alignment
The clustal W service remains one of the more popular Jalview
features.
- Muscle Multiple Alignment
High Quality and High Throughput multiple alignments of proteins. This
method can sometimes be more accurate than ClustalW when dealing with
diverse sets of sequences.
- MAFFT
Multiple Alignment with Fast Fourier Transforms - a highly accurate
and high throughput dna and amino acid alignment method, performing at
least as well as ClustalW and Muscle.
- Secondary Structure Prediction
- JNet
This is a front end to the existing JNet www server
allowing single sequence or profile based prediction.