X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fdasfeatures.html;h=1965e70471b246717556488b658e5262dee34135;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=5dc334ee28dc0777ef2c114aa433887466fe6bd9;hpb=ad0e81fcc46c354d8ae71980c5edc560fe8a6d50;p=jalview.git diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index 5dc334e..1965e70 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -1,51 +1,77 @@ - - -
DAS Sequence Feature Retrieval
-Jalview 2.1 can be set up to retrieve sequence features using the Distributed - Annotation System
-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-In some cases, the ID used to retrieve Uniprot records may be out of date - and you will be notified of that a 100% match between the sequence and a Uniprot - record was identified, but the sequence name must be manually changed (by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 Sequence Feature Retrieval +
+Jalview includes a client for retrieving sequences and their + features via the Distributed Annotation System.
+
+ 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. +
++ 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/. +
++ +