#-------------------------------------------------------------------------------
# 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
Sequence Fetcher
Jalview can retrieve sequences from certain databases using either the WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).
The Sequence Fetcher dialog box can be opened via the "File" menu on the main desktop in order to retrieve sequences as a new alignment, or opened via the "File" menu of an existing alignment to import additional sequences. Please note, there will be a short delay when the sequence fetcher is first opened, whilst Jalview compiles the list of available sequence datasources from the currently defined DAS server registry.
First, select the database you want to retrieve sequences from. Then, enter one or more accession ids (as a semi-colon separated list), or press the "Example" button to paste the example accession for the currently selected database into the retrieval box. Finally, press "OK" to initiate the retrieval.
If you are retrieving sequences from the PDB, you can retrieve
specific chains by appending a colon and the chain id to the PDB
id. For example :
1GAQ:A
If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB and PFAM) in work for publication, please cite:
Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
SOAP-based services provided by the European Bioinformatics Institute.
Nucleic Acids Res. 33(1):W25-W28 (2005)