DAS Features

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fdasfeatures.html;h=32408eed44b67ffc684b581e2f80d892f84c0917;hb=a9b2a4dd7dcbb2c86bb247970a8fe1b2ab6dc37d;hp=c2b4d49f66178254f224f2da90697c7e87be25f4;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index c2b4d49..32408ee 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -1,65 +1,77 @@ - + DAS Features -

DAS Sequence Feature Retrieval

Jalview includes a client for retrieving sequence features via -the Distributed Annotation System.

Open the Feature Settings panel by selecting "View -> - Feature Settings..."
Click on the "DAS Settings" - tabbed pane.
Select the sources to use for DAS feature retireval, then - click the "Fetch DAS Features" button. -
- Cancelling Feature Retrieval
  - Press the Cancel Fetch button to immediately stop - feature retrieval. This will not remove any features already added to - the alignment, but will halt any outstanding DAS requests.The - cancel fetch button is of particular use when one or more DAS - annotation servers are not responding! -
-

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 Sequence Identification Process

-The method of Uniprot accession id discovery is the same method which -earlier Jalview versions used for sequence feature retrieval, and is now -also used for -PDB ID discovery -. Essentially, Jalview will try to retrieve Uniprot records via the -EBI's WSDbFetch interface using each sequence's ID string (or each -string in the ID separated by the '∣' symbol). -

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 a dialog box will be opened indicating that a 100% match -between the sequence and a Uniprot record was identified, but the -sequence name is different. In this case, the ID must be manually -changed (by right clicking on the sequence ID and selecting Sequence→Edit -Name), before Jalview will show its sequence features. -

Note
- Please remember to save your alignment if either the start/end - numbering, or the sequence IDs were updated during the Uniprot ID - retrieval process.

DAS support was introduced in Jalview Version 2.1.

+ DAS Sequence Feature Retrieval +

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

Open the Feature Settings panel by selecting "View + -> Feature Settings..."
Click on the "DAS + Settings" tabbed pane. +
Select the sources to use for DAS feature retrieval, then + click the "Fetch DAS Features" button. +
- Cancelling Feature Retrieval
  Press the Cancel + Fetch button to immediately stop feature retrieval. This + will not remove any features already added to the alignment, + but will halt any outstanding DAS requests.The cancel + fetch button is of particular use when one or more DAS + annotation servers are not responding! +
+

+ 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. +

Note
Please remember to save your + alignment if either the start/end numbering, or the sequence IDs + were updated during the ID retrieval process.

+ DAS support was introduced in Jalview Version 2.1. +

+
+

+ The DAS registry at http://www.dasregistry.org was decommissioned early in 2015. An unmaintained mirror is currently hosted at http://www.ebi.ac.uk/das-srv/registry/. +