X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fdasfeatures.html;h=1965e70471b246717556488b658e5262dee34135;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=c2b4d49f66178254f224f2da90697c7e87be25f4;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index c2b4d49..1965e70 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -1,65 +1,77 @@ - +
DAS Sequence Feature Retrieval
-Jalview includes a client for retrieving sequence 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 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. -
-
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.
+
+ 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/. +
+