X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hb=801c367379086cc38bf4d3059a8e30ca9f4e78c0;hp=283377016d9183abd0b106b5b2e9d24875034697;hpb=b48eb2c8a37a5f7c4e9e361f1ebe7e44e3854cd1;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 2833770..e726c49 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,27 +1,85 @@ - -Sequence Fetcher - -

Sequence Fetcher

-

Jalview can retrieve sequences from certain databases via the -WSDBFetch service provided by the European Bioinformatics Institute.

-

A 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. -

-

Select the database you want to retrieve sequences from, and enter a - the database id (or a semi-colon separated list of several ids) in - the text 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 sequence fetcher in work for publication, then 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 + + +

+ Sequence Fetcher +

+

Jalview can retrieve sequences from a range of sequence, 3D + structure, genomic and domain family databases provided by EMBL-EBI.

+

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 contacts each database's web API.

+

+ Every time a new fetcher is opened, you will need to select + the database you want to retrieve sequences from the database + chooser. +

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

+ 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. +

+

Once you have selected a sequence database, its fetcher dialog + will open. Jalview provides two types of dialog:

+
    +
  1. The Free-text Search Interface
    Free-text + search clients are provided for PDB (Since 2.9), and UniProt + (Since 2.10). They provide access to each database's own query + system, enabling you to retrieve data by accession, free text + description, or any other type of supported field. For full + details, see each client's help page: +
    2. +
  2. Accession based sequence retrieval
    + + The Jalview Sequence Fetcher Dialog Box
    To + retrieve sequences, simply 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.
    3. +
+ +

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)

+

+ +