X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=68c552022599227a2e0096b3116beaa0f8d90351;hb=830a19575c85366f00f6025f9fe98ef8298fc289;hp=de9eac910a23e03a5baa7db50b8b083679cffd8d;hpb=dfabc2facf04bc805f0b6001b94de3c62b3049b0;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index de9eac9..68c5520 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,46 +1,68 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Sequence Fetcher

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" +WSDBFetch service provided by the European Bioinformatics Institute, or, 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" 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.

-

+

Since Jalview 2.x.x if PDB is selected as the sequence database, a specialised interface - PDB Sequence Fetcher is used for discovering and retrieving the sequenec data.

+

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