X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=ab222dff0212dbe29d7c958a365963c41dc16d38;hp=02ff94ed7cdf32d44b3444dd073f613fd9ce4042;hpb=f7fd2fcf425c4a599dbb1440678672eb31cd865a;p=jalview.git
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
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@@ -1,19 +1,107 @@
-
-Sequence Fetcher
-
-Sequence Fetcher
-The Sequence Fetcher can be started from the main desktop "File"
- menu or from a particular alignment window.
-Select which database to fetch your sequence from and enter the sequence id.
- If you are retrieving sequences from PDB database and you know which chain you
- would like to retrieve, append the chain id after colon to the PDB id. eg 1GAQ:A
-The Sequence Fetcher uses WSDBFetch provided by the European Bioinformatics
- Institute. If you use this service please quote:
-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
+
+
+
+ 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)
+
+
+