X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;fp=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html deleted file mode 100755 index e726c49..0000000 --- a/help/html/features/seqfetch.html +++ /dev/null @@ -1,85 +0,0 @@ - - - -Sequence Fetcher - - -

- Sequence Fetcher -

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

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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.

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- 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. -

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

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    -
  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:

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- 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)

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