Sequence Features

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfeatures.html;h=3c9d2b84d33f11b9b8e75ed67611082e89b5a067;hb=8ec36c3e36ff5beb0db07345babe8c8426d0426b;hp=4026071ed64c7fc7b04e08efa26cbbb5ab672195;hpb=92ae1457a784553ccdb842b122d481ce6c5ff24f;p=jalview.git diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 4026071..3c9d2b8 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -1,43 +1,111 @@ - -Sequence Features - -

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! -
-
- 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.
- - + + + +Sequence Features + + +
+ Sequence Features +
+
+ Jalview can colour parts of a sequence based on the presence of + sequence features - which may be retrieved from database records + (such as UniProt), the result of sequence + motif searches or simply read from a sequence + features file. You can also create + features from the results of searches or the current selection, + and edit features by double + clicking on them. +
+
+ Sequence Feature Colouring Styles +
+
+ By default, Jalview will assign a color to each feature based on its + type. These colours can be changed from the feature settings and amend features dialog boxes. Since + Jalview 2.5, it is also possible to define feature colourschemes to shade + features based on their associated scores or text labels. +
+
+ Sequence Feature Groups +
+
+ Since Jalview 2.08, sequence features assigned to a sequence can be + organised into groups, which may indicate that the features were all + retrieved from the same database (such as UniProt features), or + generated by the same analysis process (as might be specified in a sequence features file). +
+
+ Sequence Feature Inheritance +
+
+ Since Jalview 2.08, sequence features are global to a set + of sequences appearing (independently or together) in many different + alignments. Practically, this means features loaded onto one + alignment can be viewed in any alignments involving the same + sequences. The same sequence appears in different alignments when a + new alignment is generated by submitting an existing set of + sequences to one of the alignment or prediction web services, and + when sequences are copied and pasted into other alignment windows. +
+
+ View→Show Sequence Features +
+
Toggle the display of sequence features in this alignment. If + 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.
+ Since Jalview 2.1, it is possible to add DAS + features to an alignment via the DAS tabbed pane of the feature + settings window. +
+
+ View→Sequence ID Tooltip→Show + Non-Positional features
Only available in + application
+
+
Toggles the display of non-positional features in the sequence + ID tooltip, and whether they will be included when sequence features + are exported using "File→Export Features".
+
+ 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 more + details. +
+ +