X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hb=b39ce946e3f05bcf923abc266df2ef33be95a672;hp=a956d6d1148339ccf1ef1ac1f70cbc56fda52009;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index a956d6d..e726c49 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -1,53 +1,85 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Sequence Fetcher
-Jalview can retrieve sequences from certain databases using either the -WSDBFetch service provided by the European Bioinformatics Institute, and, 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. Please note, there will 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. Then, 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 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
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)
-
+
+ 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:
+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)