X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=54dd5d7c3c4384ef383ead7cf3d150ac5fddb3da;hp=a51aa9599b4fac0a72c261c08c9e43478c6a1b40;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
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@@ -1,72 +1,107 @@
+ * 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.
-Fetching Individual PDB Chains
-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- -
Retrieving parts of large sequence records
-When retrieving from DAS sequence sources, coordinate range arguments
-can be passed to the server using the standard DAS sequence command
-format:
- <AccessionId>:<start>,<end>If you know a source -understands this type of query format, then you should untick the -checkbox for 'replace commas with semi-colons' so the range query can be -passed to the server; otherwise, the query will be split into two (e.g -'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases, -however, a source that supports range queries will include a range -qualification in its example query, and Jalview will then automatically -disable the 'replace commas with semi-colons' option.
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)
+