The Alignment Annotations File

The Alignment Annotations File

Alignment annotations can be imported onto an alignment since version 2.08 of Jalview, via an annotations file. It is a simple ASCII text file consisting of tab delimited records similar to the Sequence Features File, and introduced primarily for use with the Jalview applet.

Alignment annotations files are imported into Jalview in the following ways:

from the command line
-annotations <Annotations filename>
Dragging an annotations file onto an alignment window
Via the "Load Features / Annotations" entry in the File menu of an alignment window.

Annotations File Format

The File consists of lines containing an instruction followed by tab delimited fields, and any lines starting with "#" are ignored. The first non-commented out line of a valid Annotations file must begin with :

JALVIEW_ANNOTATION

A row of annotation is added with a line like

GRAPH_TYPE	Label	Values

The GRAPH_TYPE field, which appears first, defines the appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. The final Values field contains a series of "|" separated value fields. Each value field is itself a comma separated list of fields of a particular type defined by the annotation row's GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "|" symbol) are shown below:

BAR_GRAPH
Plots a histogram with labels below each bar.
number,text character
LINE_GRAPH
Draws a line between values on the annotation row.
number
NO_GRAPH
For a row consisting of text labels and/or secondary structure symbols.
{Secondary Structure Symbol},text label
Currently supported secondary structure structure symbols are H (for helix) and E (for strand)

Any or all value fields may be left empty, as well as the BAR_GRAPH's text character field, and either or both of the text-label and secondary structure symbol fields of the NO_GRAPH type annotation rows.

You can associate an annotation with a sequence by preceding its definition with the line:

SEQUENCE_REF	seq_name	[startIndex]

All Annotations defined after a SEQUENCE_REF command will then be associated with that sequence, and the first field in the Value field list will (optionally) be placed at the startIndex'th column.

New in Jalview 2.4

Sequence associations are turned off for subsequent annotation definitions by:

SEQUENCE_REF	ALIGNMENT

LINE_GRAPH type annotations can be given a colour (specified as 24 bit RGB triplet in hexadecimal or comma separated values), combined onto the same vertical axis, and have ordinate lines (horizontal lines at a particular vertical axis value) using the following commands (respectively):

COLOUR	graph_name	colour
COMBINE	graph_1_name	graph_2_name
GRAPHLINE	graph_name	value	label	colour

(Since Jalview 2.2.1) SEQUENCE_GROUP

Groups of sequences can be defined using the tab delimited line

SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	Sequences

The sequences can be defined by alignment index and a range of sequences can be defined in a comma delimited field such as

2-5,8-15,20,22

Enter * to select all groups.

If the alignment indices are not known, enter -1 then a tab delimited list of sequence ids.

If the SEQUENCE_REF has been defined, the group_start and group_end will be relative to the sequence residue numbering, otherwise the group_start and group_end will be the alignment column indices.

The group can (optionally) be assigned various visualisation properties via another tab delimited line thus:

PROPERTIES	Group_name	tab_delimited_key_value_pairs

The key_value_pairs allow you to define a description and to colour the group in various ways. All, none or some of the following values could be used for a group:

description=Text
colour=Helix Propensity
pidThreshold=0
consThreshold=0
outlineColour=red
displayBoxes=true
displayText=false
colourText=false
textCol1=black
textCol2=black
textColThreshold=0
idColour=ff3322

New Features in 2.4:

if the idColour property is given without specifying a colour scheme with the colour property, then the idColour will also be used to colour the sequence.
the colour property can take either a colour scheme name, or a single colour specification (either a colour name like 'red' or an RGB triplet like 'ff0066'). If a single colour is specified, then the group will be coloured with that colour.

An example Annotation file is given below:

#Comment lines follow the hash symbol
JALVIEW_ANNOTATION
SEQUENCE_REF	FER1_MESCR	5
BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
COLOUR	Bar Graph 2	blue
COLOUR	Red Values	255,0,0
COLOUR	Green Values	green
COLOUR	Purple Letters	151,52,228
COMBINE	Green Values	Red Values
GRAPHLINE	Red Values	2.6	threshold	black

SEQUENCE_GROUP Group_A 30 50 *
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1	seq2	seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false	colourText=false textCol1=black textCol2=black textColThreshold=0
PROPERTIES Group_B outlineColour=red
PROPERTIES Group_C colour=Clustal