X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=b7b29fb6c0b015ac4798ec4718ab0cfbdd79b20a;hp=ff5c1b0944aac1516cee9e12936b0b524d5d89d8;hpb=d0771875f23ab994c4f85fb6cd604378768df10e;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index ff5c1b0..44aa1c2 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -32,58 +32,66 @@ 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. 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.

+

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 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. + 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) -

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.

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

- 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. + 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. +
+ If you have DAS sources enabled, then you may have several + sources for the same type of sequence identifier, and these will + be grouped together in a sub-branch branch labeled with the + identifier.

+

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. +

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 + When using DAS sources (indicated by a "(DAS)"), + you can append a range in addition to a sequence ID. For example, 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,