X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hb=801c367379086cc38bf4d3059a8e30ca9f4e78c0;hp=02ff94ed7cdf32d44b3444dd073f613fd9ce4042;hpb=f7fd2fcf425c4a599dbb1440678672eb31cd865a;p=jalview.git
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index 02ff94e..e726c49 100755
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@@ -1,19 +1,85 @@
-
-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 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:
+
+ - 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.
+
+
+ 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)
+
+
+