Sequence Fetcher
Jalview can retrieve sequences from a range of sequence, 3D structure, genomic and domain family databases provided by EMBL-EBI.
The Sequence Fetcher 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. There may be a short delay when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.
Every time a new fetcher is opened, you will need to select the database you want to retrieve sequences from the database chooser.
The databases are shown as a tree, and ordered alphabetically; tooltips are shown if you mouse over some sources, explaining what the database will retrieve. You can select one by using the up/down arrow keys and hitting return, or by double clicking with the mouse.
Once you have selected a sequence database, its fetcher dialog will open. Jalview provides two types of dialog:
If you use the WSDBFetch sequence fetcher services (EMBL, UniProt, 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.
SOAP-based services provided by the European
Bioinformatics Institute.
Nucleic Acids Res. 33(1):W25-W28
(2005)