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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Sequence Fetcher
-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.
-Fetching Individual PDB Chains
-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
-
-Retrieving parts of large sequence records
-When retrieving from DAS sequence sources, coordinate range arguments
-can be passed to the server using the standard DAS sequence command
-format:
- <AccessionId>:<start>,<end>
If you know a source
-understands this type of query format, then you should untick the
-checkbox for 'replace commas with semi-colons' so the range query can be
-passed to the server; otherwise, the query will be split into two (e.g
-'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases,
-however, a source that supports range queries will include a range
-qualification in its example query, and Jalview will then automatically
-disable the 'replace commas with semi-colons' option.
-The option to disable the comma to semi-colon translation was
-added in Jalview 2.6
-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)
-
-
+
+ Sequence Fetcher
+
+
+ Jalview can retrieve sequences from certain databases using either
+ the DBFetch service provided by the EMBL European Bioinformatics
+ Institute, or, since Jalview 2.4, DAS servers capable of the sequence
+ command (configured in DAS settings).
+
+ 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 compiles
+ the list of available sequence datasources from the currently
+ defined DAS server registry.
+
+ 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.
+
+ If you have DAS sources enabled, then you may have several
+ sources for the same type of sequence identifier, and these will
+ be grouped together in a sub-branch branch labeled with the
+ identifier.
+
+ Once you have selected a sequence database, its fetcher dialog
+ will open. Jalview provides two types of dialog:
+
+ - The Free-text Search Interface
Free-text
+ search clients are provided for PDB (Since 2.9), and UniProt
+ (Since 2.10). They provide access to each database's own query
+ system, enabling you to retrieve data by accession, free text
+ description, or any other type of supported field. For full
+ details, see each client's help page:
+
+ - Accession based sequence retrieval
+
+
To
+ retrieve sequences, simply 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.
+
+
+ Only retrieving part of a sequence
+
+
+ When using DAS sources (indicated by a "(DAS)"),
+ you can append a range in addition to a sequence ID. For example, 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, 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)
+