From 3b58e33030c6cfe56564d17edcb9d81b750398fe Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 14 Aug 2006 15:22:36 +0000 Subject: [PATCH] 2.1 updates --- help/help.jhm | 1 + help/helpTOC.xml | 2 +- help/html/features/seqfeatures.html | 55 +++++------------------------------ 3 files changed, 10 insertions(+), 48 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index 3790abe..8c314d3 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -26,6 +26,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 9265599..d08e3d2 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -19,7 +19,7 @@ - + diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 5283e38..9efa19f 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -27,53 +27,14 @@ and pasted into other alignment windows.

feature retrieval has not already been carried out, then Jalview will automatically try to fetch sequence features (as described below).

View→Sequence Feature Settings... -

Once sequence features have been loaded, their display can be fully - controlled using the alignment window's Sequence Feature Settings dialog - box. Feature colour schemes and display parameters are unique to a - particular alignment, so it is possible to colour the same sequence - features differently in different alignment views.

-

View→Fetch Sequence Features

-

When this option is selected, sequence features extracted from the - Uniprot (http://www.ebi.unprot.org/index.html) - record for each sequence are displayed on the alignment.

-

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.

-

More information about the feature is given in a tooltip, which is viewed by - moving the mouse pointer over a sequence feature. The description associated - with the feature will then be displayed in a small label near the pointer.

-

The Sequence Identification Process - -

-

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. -

    -
  • remember to save your alignment if you have updated any of the sequence - IDs!
    • -
+

Once sequence features have been loaded, their display can be fully controlled + using the alignment window's Sequence Feature Settings dialog box. Feature + colour schemes and display parameters are unique to a particular alignment, + so it is possible to colour the same sequence features differently in different + alignment views.
+ Since Jalview 2.1, it is possible to add DAS features + to an alignment via the DAS tabbed pane of the feature settings window.

Precalculated Sequence Features may be added to an alignment from the command line, drag and drop, or from the "File->Load Features / Annotations" menu item. See the Features File Format for -- 1.7.10.2