X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=e502a7571bf01a0354ce8205948dd7a3cda1603b;hp=135e4d57d49bb877c74c3895c9eecd41321bfab6;hpb=169747b5aac00cb86214916fdfc653a2be26ed92;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 135e4d5..44aa1c2 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,34 +1,107 @@ -
Sequence Fetcher
-Jalview can retrieve sequences from certain databases using either the -WSDBFetch service provided by the European Bioinformatics Institute, and DAS servers capable of the sequence command (since version 2.4).
- -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 and PFAM) - 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 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" + 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.
++ 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.
+
+ 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 +
+
+ 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:
+
+ 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)