Sequence Features File Format
-(Prior to version 2.08 known as the "Groups file")
- A precalculated Features file can read onto an alignment from the command line
- ("-features"), by drag and dropping the features file onto an alignment
- or by selecting from the File menu "Load Features / Annotations".
Specify the feature types first, then refer to the feature type for each sequence.
-featureType<tab>colour
- description<tab>sequenceId<tab>sequenceIndex<tab>start<tab>end<tab>featureType
eg
- domain red
- metal ion-binding site 00ff00
- transit peptide 0,105,215
- chain 225,105,0
- modified residue 105,225,35
- signal peptide 0,155,165
- Your Own description here FER_CAPAA -1 3 93 domain
- Your Own description here FER_CAPAN -1 48 144 chain
- Your Own description here FER_CAPAN -1 50 140 domain
- Your Own description here FER_CAPAN -1 136 136 modified residue
- Your Own description here FER1_LYCES -1 1 47 transit peptide
- Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide
- Your Own description here Q93XJ9_SOLTU -1 49 144 chain
An additional option in Jalview 2.08 is to group features in the following - way:
-STARTGROUP<tab>My feature groupA
- ....Many Feature descriptions here
- ENDGROUP<tab>My feature groupA
-
+ Sequence Features File +
+
The Sequence features file (which used to be known as the + "Groups file" prior to version 2.08) is a simple way of getting your + own sequence annotations into Jalview. It was introduced to allow + sequence features to be rendered in the Jalview applet, and so is + intentionally lightweight and minimal because the applet is often + used in situations where data file size must be kept to a minimum, + and no XML parser is available.
+ +
+ Features files are imported into Jalview in the following ways:
+
+ -features <Features filename> ++
+ Sequence Features File Format +
++ A features file is a simple ASCII text file, where each line + contains tab separated text fields. No comments are + allowed. +
++ Feature Colours +
+The first set of lines contain feature type definitions and their colours: +
+Feature label Feature Colour + ++ + A feature type has a text label, and a colour specification. This can + be either: + +
+[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]] +The fields are as follows: + +
+ Feature Filters +
+This section is optional, and allows one or more filters to be defined for each feature type.
+
Only features that satisfy the filter conditions will be displayed.
+
Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS.
+
Each line has the format:
+
featureType <tab> (filtercondition1) [and|or] (filtercondition2) [and|or]...+ The parentheses are not needed if there is only one condition. + Combine multiple conditions with either and or or (but not a mixture). +
Label or Score or AttributeName condition [value]+ where either the label (description), (numeric) score, or (text or numeric) attribute is tested against the condition. +
+ Feature Instances +
+ +The remaining lines in the file are the sequence annotation + definitions, where the now defined features are attached to regions + on particular sequences. Each feature can optionally include some + descriptive text which is displayed in a tooltip when the mouse is + near the feature on that sequence (and may also be used to generate + a colour for the feature).
+ ++ If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or + GFF3 + (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format, + then you can leave it as is, after first adding a line containing only + 'GFF' after any Jalview feature colour definitions (this + mixed format capability was added in Jalview 2.6). Alternately, + you can use Jalview's own sequence feature annotation format, which + additionally allows HTML and URLs to be directly attached to each + piece of annotation. +
+ ++ Jalview's sequence feature annotation format +
+Each feature is specified as a tab-separated series of columns + as defined below: +
+description sequenceId sequenceIndex start end featureType score (optional) ++ + This format allows two alternate ways of referring to a sequence, + either by its text ID, or its index (base 0) in an associated + alignment. Normally, sequence features are associated with sequences + rather than alignments, and the sequenceIndex field is given as + "-1". In order to specify a sequence by its index in a + particular alignment, the sequenceId should be given as + "ID_NOT_SPECIFIED", otherwise the sequenceId field will be + used in preference to the sequenceIndex field. + + + +
+ The description may contain simple HTML document body tags if
+ enclosed by "<html></html>" and these will be
+ rendered as formatted tooltips in the Jalview Application (the
+ Jalview applet is not capable of rendering HTML tooltips, so all
+ formatting tags will be removed).
Attaching Links
+ to Sequence Features
Any anchor tags in an html formatted
+ description line will be translated into URL links. A link symbol
+ will be displayed adjacent to any feature which includes links, and
+ these are made available from the links submenu
+ of the popup menu which is obtained by right-clicking when a link
+ symbol is displayed in the tooltip.
Non-positional
+ features
Specify the start and end for
+ a feature to be 0 in order to attach it to the
+ whole sequence. Non-positional features are shown in a tooltip when
+ the mouse hovers over the sequence ID panel, and any embedded links
+ can be accessed from the popup menu.
Scores
+ Scores can be associated with sequence features, and used to sort
+ sequences or shade the alignment (this was added in Jalview 2.5).
+ The score field is optional, and malformed scores will be ignored.
+
Feature annotations can be collected into named groups by + prefixing definitions with lines of the form: +
+startgroup groupname ++ + .. and subsequently post-fixing the group with: + +
+endgroup groupname ++ + Feature grouping was introduced in version 2.08, and used to control + whether a set of features are either hidden or shown together in the + sequence Feature settings dialog box. + + + +
A complete example is shown below : +
+domain red +metal ion-binding site 00ff00 +transit peptide 0,105,215 +chain 225,105,0 +modified residue 105,225,35 +signal peptide 0,155,165 +helix ff0000 +strand 00ff00 +coil cccccc +kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0 + +STARTFILTERS +metal ion-binding site Label Contains sulfur +kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8) +ENDFILTERS + +Your Own description here FER_CAPAA -1 3 93 domain +Your Own description here FER_CAPAN -1 48 144 chain +Your Own description here FER_CAPAN -1 50 140 domain +Your Own description here FER_CAPAN -1 136 136 modified residue +Your Own description here FER1_LYCES -1 1 47 transit peptide +Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide +Your Own description here Q93XJ9_SOLTU -1 49 144 chain + +STARTGROUP secondarystucture +PDB secondary structure annotation FER1_SPIOL -1 52 59 strand +PDB secondary structure annotation FER1_SPIOL -1 74 80 helix +ENDGROUP secondarystructure + +STARTGROUP kd +Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8 +ENDGROUP kd + +GFF +FER_CAPAA GffGroup domain 3 93 . . ++ + +