X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=4aa72344b9981ffde1892f522dc7eafd6f868c74;hb=1f46c912a14d05f673e19b272fec4e6094874fa5;hp=c4d671aa59d729820cbdc8e3ffed27858c3a80a6;hpb=152aa52bc19a393141cfc19f5852d1fbcd239f16;p=jalview.git
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index c4d671a..4aa7234 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -1,74 +1,99 @@
+ * 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
-Some sequence sources allow a range query to be appended to the sequence
-ID - e.g. 'Mito:1,85779'. 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 up into two 'Mito:1' and '85779'). In
-some cases, a source that supports range queries usually include a range
-qualification in its example query. In this case, Jalview will
-automatically disable the 'replace commas with semi-colons' option.
-Support for range queries was added in Jalview 2.6
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 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. +
++ 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. +
++ 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, 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)
+