X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fdasfeatures.html;h=16351835fb162cb79cfc1f9c4053a067393c3078;hb=d1d6724c7a22a6955f0a1213686f56e254b68546;hp=5dc334ee28dc0777ef2c114aa433887466fe6bd9;hpb=ad0e81fcc46c354d8ae71980c5edc560fe8a6d50;p=jalview.git diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index 5dc334e..1635183 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -1,51 +1,65 @@ - - -DAS Features - - -

DAS Sequence Feature Retrieval

-

Jalview 2.1 can be set up to retrieve sequence features using the Distributed - Annotation System

-
    -
  1. Open the Feature Settings panel by selecting "View -> Feature Settings..."
    2. -
  2. Click on the "DAS Settings" tabbed - pane.
    3. -
  3. Select the sources to use for DAS feature retireval, then click the "Fetch - DAS Features" button.
    4. -
-

If your DAS source selection contains sources which use Uniprot accession ids, - you will be asked whether Jalview should find Uniprot Accession ids for the - given sequence names. It is important to realise that many DAS sources only - use Uniprot accession ids, not names of sequences.
- The method of Uniprot accession id discovery is the same method which earlier - Jalview versions used for sequence feature retrieval, ie WSDbFetch provided - by the EBI.

-

The process is as described:

-

The Sequence Identification Process

-

Jalview will attempt to retrieve sequence features from Uniprot files using - the EBI dbFetch web service using the given sequence names (or Uniprot ID, if - available). A 100% match with the Uniprot record is required for Uniprot features - to be view on a sequence.

-

The first step in the procedure for matching uniprot IDs to sequences is to - use the ID (name) of each sequence to retrieve Uniprot records directly.

-

If a uniprot record (or set of records) is found for a sequence, then the - sequence is aligned to the one in the Uniprot record to determine the correct - start and end residue positions (which are displayed when the 'Show Full Sequence - ID' option is set).

-

If the alignment reveals differences between the sequence in the alignment - and the one in the record, then Jalview will assume that the aligned sequence - is not the one in the uniprot record.

-

In some cases, the ID used to retrieve Uniprot records may be out of date - and you will be notified of that a 100% match between the sequence and a Uniprot - record was identified, but the sequence name must be manually changed (by right - clicking on the sequence ID and selecting Sequence→Edit Name), - before Jalview will show its sequence features. -

-

  -

-

  - - + + + +DAS Features + + + +

DAS Sequence Feature Retrieval

+

Jalview includes a client for retrieving sequences and their features via +the Distributed Annotation System.

+
    +
  1. Open the Feature Settings panel by selecting "View -> + Feature Settings..."
    2. +
  2. Click on the "DAS Settings" + tabbed pane.
    3. +
  3. Select the sources to use for DAS feature retrieval, then + click the "Fetch DAS Features" button. + +
    4. +
+

If your DAS source selection contains sources which use Uniprot +accession ids, you will be asked whether Jalview should find Uniprot +Accession ids for the given sequence names. It is important to realise +that many DAS sources only use Uniprot accession ids, rather than +Swissprot/Uniprot sequence names.
+The database reference +fetcher documentation describes how Jalview discovers what database +references are appropriate for the sequences in the alignment. +

+

  +

DAS support was introduced in Jalview Version 2.1.

+

  + +