From c8a1ca18b183b2352554661b713d2cd600addb68 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 21 Dec 2007 15:08:26 +0000 Subject: [PATCH] automatic dbref fetching and sequence validation for arbitrary databases --- help/html/features/dasfeatures.html | 27 +++------------- help/html/webServices/dbreffetcher.html | 52 +++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+), 23 deletions(-) create mode 100644 help/html/webServices/dbreffetcher.html diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index c2b4d49..3f2674e 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -30,32 +30,13 @@ 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. +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 Uniprot ID + numbering, or the sequence IDs were updated during the ID retrieval process.

diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html new file mode 100644 index 0000000..98300aa --- /dev/null +++ b/help/html/webServices/dbreffetcher.html @@ -0,0 +1,52 @@ + + + +Database Reference Fetching + +

Discovering Database References for Sequences
+Database references are associated with a sequence are displayed as a +list in the tooltip shown when mousing over its sequence ID. Jalview +uses references for the retrieval of PDB structures and DAS features, and for +retrieving sequence cross-references such as the protein products of a +DNA sequence.

Jalview discovers references for a sequence by generating a set +of ID queries from the ID string of each sequence in the alignment. It +then tries to query all the databases it can access in order to match +the alignment sequence to any records retrieved from the database. If a +match is found, then the sequence is annotated with that database's +reference, and any cross-references that it's records contain.

The Sequence Identification Process
+The method of accession id discovery is derived from the method which +earlier Jalview versions used for Uniprot sequence feature retrieval, +and was originally restricted to the identifaction of valid Uniprot +accessions.
+Essentially, Jalview will try to retrieve records from all the databases +accessible by the sequence +fetcher using each sequence's ID string (or each string in the ID +separated by the '∣' symbol).

If a record (or set of records) is retrieved by any query derived +from the ID string of a sequence, then the sequence is aligned to the +ones retrieved to determine the correct start and end residue positions +(which are displayed when the 'Show Full Sequence ID' option). This is +important for the correct display of the location of any features +associated with that database.

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 retrieved record.

In some cases, the ID used to retrieve records may be out +of date and a dialog box will be opened indicating that a 100% match +between the sequence and the record was identified, but the +sequence name is different. In this case, the can be manually +changed (by right clicking on the sequence ID and selecting Sequence→Edit +Name). +

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

+ + \ No newline at end of file -- 1.7.10.2