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.
-The first set of lines contain type definitions:
-Feature label Feature Colour
-A feature type has a text label, and a colour (specified as a
-red,green,blue 24 bit triplet either in hexadecimal (eg. 00ff00) or as comma
-separated numbers (ranging from 0 to 255)).
-
The remaining lines in the file are the sequence annotation -definitions, where the now defined features are attached to regions on -particular sequences, optionally with some descriptive text (displayed -in a tooltip when the mouse is near the feature on that sequence). There are two alternate ways of referring to a -sequence, either by its text ID, or its index in an associated -alignment.
-description sequenceId sequenceIndex start end featureTypeNormally, -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.
-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 -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 -- - - - + + + + +
+ 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. +
+The first set of lines contain type definitions: +
+Feature label Feature Colour + ++ + A feature type has a text label, and a colour specification. This can + be either: + +
+[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]] +The fields are as follows: + +
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 can also be used to generate + a colour the feature).
+ ++ If your sequence annotation is already available in GFF Format (see + http://www.sanger.ac.uk/resources/software/gff/spec.html), + 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 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 +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 +GFF +FER_CAPAA GffGroup domain 3 93 . . ++ + +