X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=936ac942e96e2767e1b1fff46e805e8a1e5be1c7;hp=4aa72344b9981ffde1892f522dc7eafd6f868c74;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 4aa7234..44aa1c2 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -32,62 +32,70 @@ 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.
+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.
- 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. + Every time a new fetcher is opened, you will need to select + the database you want to retrieve sequences from the database + chooser.
- -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 -
-
- Since Jalview 2.9, selecting PDB as the sequence database will open
- the PDB Sequence Fetcher for
- discovering and retrieving structures.
+ 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:
+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:
+ 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