From: jprocter Date: Sun, 2 Sep 2012 14:12:01 +0000 (+0100) Subject: JAL-1075 JAL-1062 documentation and new figure for db selection dialog X-Git-Tag: Jalview_2_9~355 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=86b15b81cbb0207bcc1eff8480b08e1b45bb6452 JAL-1075 JAL-1062 documentation and new figure for db selection dialog --- diff --git a/help/html/features/selectfetchdb.gif b/help/html/features/selectfetchdb.gif new file mode 100644 index 0000000..6e1ce10 Binary files /dev/null and b/help/html/features/selectfetchdb.gif differ diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index a956d6d..e56fa7b 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -23,24 +23,42 @@

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 Jalview Sequence Fetcher Dialog Box -

The Sequence Fetcher dialog box can be opened via the "File" + The Jalview Sequence Fetcher Dialog Box +

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, + 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. + currently defined DAS server registry.

-

First, select the database you want to retrieve sequences from. Then, enter +

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.

+ Database selection dialog for fetching sequences (introduced in Jalview 2.8) +

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

When retrieving from DAS sequence sources, - coordinate range arguments can be passed to the server using the standard DAS - sequence command format (:<start>,<end>)

+ id. For example :
 1GAQ:A
+

+

+ 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 diff --git a/help/html/features/seqfetcher.gif b/help/html/features/seqfetcher.gif index 652976f..03ddd79 100644 Binary files a/help/html/features/seqfetcher.gif and b/help/html/features/seqfetcher.gif differ