Sequence Features

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfeatures.html;h=4026071ed64c7fc7b04e08efa26cbbb5ab672195;hb=92ae1457a784553ccdb842b122d481ce6c5ff24f;hp=160c1e27ffaa19ba81a39f3bfeb49557aba29a6e;hpb=674835f42bf25bf22ccc51d067c4dc16e0ab4601;p=jalview.git diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 160c1e2..4026071 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -1,22 +1,43 @@ Sequence Features -

Sequence Features

This displays Uniprot sequence features on the alignment if a 100% sequence - match is found.

The first step in this process is to match the id (name) of each sequence with - Uniprot. If there is no match, a Blast search is performed to try to obtain - the Uniprot Id for each sequence. You will be notified of any 100% matches with - Uniprot, which you must manually assign to each sequence in your input alignment, - then save the file.

View→Sequence Features

When this option is selected, sequence features extracted from the + Uniprot record for each + sequence are displayed on the alignment.

Currently, sequence features are rendered in red or blue, dependent + upon their type:

Features associated with a particular residue are coloured + red
e.g. an active site residue
Features which span a region are coloured blue
+e.g. a region of sequence with known structure
+
More information about the feature is given in a tooltip, which are + viewed by moving the mouse pointer over a sequence feature. The + associated text for the feature will then be displayed in a small + label will appear near the pointer.
+
After the Sequence Features option is selected, there may be some delay before + the features are actually rendered, as jalview must first determine if a + sequence is contained in uniprot and then retrieve its sequence + record. This delay should only happen once for a particular + alignment, as jalview caches uniprot records in a file in your home + directory called '.jalview.uniprot.xml'. + +
The first step in this process is to try to use the ID (name) of + each sequence as an ID search in Uniprot. If there is no match, The + EBI Blast search is used in an attempt to obtain the Uniprot Id for + each sequence. You will be notified of any 100% matches with + Uniprot, but you must then manually change the name of the sequence, + 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! +
- The input sequence will be matched with the returned Uniprot record, the start - and end residues can then be correctly assigned to each sequence.
-
Sequence features which are 1 residue in length are coloured red. Features - which span a region are coloured blue.
-
By moving the mouse pointer over a sequence feature on the alignment a small - label will appear with the description of that sequence feature.
-
A local cache of retrieved uniprot entries is recorded on your local machine. -
+ If a uniprot record (or set of records) is found for a sequence, + then the sequence in aligned to the one in the Uniprot record + to determine the correct start and end residue positions that will be + displayed when the 'Show Full Sequence ID' option is set.