X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;fp=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hb=20a4d7ddb86ee996f2b6617a0470922b83354c35;hp=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hpb=5610d0f46a76d4269d25148d42f92d867fa1061a;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 44aa1c2..e726c49 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -26,19 +26,13 @@
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" +
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 compiles - the list of available sequence datasources from the currently - defined DAS server registry.
+ 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
@@ -51,11 +45,6 @@
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:
@@ -82,17 +71,6 @@ 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: