X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=978ff69a2fa5b918f8c39c10c0536f2872c8df27;hp=89b3d3bb65c1be2d052ac55675ae2c5e115f66be;hpb=11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9;p=jalview.git
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
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@@ -23,60 +23,85 @@
Sequence Fetcher
-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 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. 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.
-
- 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.
- 
- 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.
- Fetching from The PDB with the EMBL-EBI PDBe Search
- Interface
+ Sequence Fetcher
- Since Jalview 2.9, selecting PDB as the sequence database will open
- the PDB Sequence Fetcher for
- discovering and retrieving structures.
+ 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
- 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
+ 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)
-
+
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)