Sequence Fetcher
Jalview can retrieve sequences from certain databases using either the -WSDBFetch service provided by the European Bioinformatics Institute, and DAS servers capable of the sequence command (since version 2.4).
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-The Sequence Fetcher dialog box can be opened via the "File" +WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).
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+ 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, + to import additional sequences. There may 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. + currently defined DAS server registry.
-First, select the database you want to retrieve sequences from. Then, enter +
First, select the database you want to retrieve sequences from + by clicking the button labeled 'Select database retrieval source'. If + a database source is already selected, then the button's label will + change to show the currently selected database.
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+ Since Jalview 2.8, the + available databases are shown as a tree in a popup dialog box. The + databases are ordered alphabetically, and if there are many sources + for the same type of sequence identifier, they will be grouped + together in a sub-branch branch labeled with the identifier.
+Once you have selected the sequence database using the popup dialog box, 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.
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Specifying chains for PDB IDs
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)
+ id. For example :
1GAQ:A+ +
+ Only retrieving part of a sequence DAS sources
+ (indicated by a "(DAS)") allow a range to be
+ specified in addition to a sequence ID. To retrieve 50 residues
+ starting at position 35 in UNIPROT sequence P73137 using the UNIPROT
+ DAS server, you would enter "'P73137:35,84'.
Full support for DAS range queries was introduced in Jalview 2.8
+
If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM) 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.