X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hb=b39ce946e3f05bcf923abc266df2ef33be95a672;hp=fa61e1ac6404e01c72cc2bcc4c91ae6c5ac5a153;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index fa61e1a..e726c49 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -23,52 +23,63 @@
Sequence Fetcher
-Jalview can retrieve sequences from certain databases using either the -WSDBFetch service provided by the 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.
-Specifying chains for PDB IDs
- If you are retrieving sequences from the PDB, you can retrieve
- specific chains by appending a colon and the chain id to the PDB
- id. For example :
1GAQ:A+
+ Sequence Fetcher
-
- 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
-
If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, 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)
-
+
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:
+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)