3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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23 <meta name="generator" content="HTML Tidy, see www.w3.org">
24 <title>Sequence Features File</title>
27 <p><strong>Sequence Features File</strong><p>
29 The Sequence features file (which used to be known as the
30 "Groups file" prior to version 2.08) is a simple way of getting
31 your own sequence annotations into Jalview. It was introduced to
32 allow sequence features to be rendered in the Jalview applet, and
33 so is intentionally lightweight and minimal because the applet is
34 often used in situations where data file size must be kept to a
35 minimum, and no XML parser is available.</p>
37 <p>Features files are imported into Jalview in the following
41 <li>from the command line
44 <strong> -features <<em>Features filename</em>></strong>
48 <li>Dragging a features file onto an alignment window</li>
50 <li>Via the "Load Features / Annotations" entry in the
51 <strong>File</strong> menu of an alignment window.</li>
56 <p><strong>Sequence Features File Format</strong></p>
58 A features file is a simple ASCII text file, where each line
59 contains tab separated text fields. <strong>No comments are
62 The first set of lines contain type definitions:
65 <strong><em>Feature label</em>	<em>Feature Colour</em>
66 <!-- 	<em>Feature links</em> --></strong>
69 A feature type has a text label, and a colour specification. This
73 <li>A single colour specified as either a red,green,blue 24 bit
74 triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
75 (ranging from 0 to 255))</li>
77 <li>A <a href="featureschemes.html">graduated colourscheme</a>
78 specified as a "|" separated list of fields:
81 [label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
84 The fields are as follows:
87 <li><em>label</em><br>
88 Indicate that the feature description should be used to create a
89 colour for features of this type.<br>
90 <em>Note: if no threshold value is needed then the final '|' may be
92 This keyword was added in Jalview 2.6</em></li>
94 <li><em>mincolor</em> and <em>maxcolor</em><br>
95 Colour triplets specified as hexadecimal or comma separated values
96 (may be left blank for a <em>label</em> style colourscheme, but
97 remember to specify the remaining fields)</li>
99 <li><em>absolute</em><br>
100 An optional switch indicating that the <em>minvalue</em> and
101 <em>maxvalue</em> parameters should be left as is, rather than
102 rescaled according to the range of scores for this feature
105 <li><em>minvalue</em> and <em>maxvalue</em><br>
106 Minimum and maximum values defining the range of scores for which
107 the colour range will be defined over. If minvalue is greater than
108 maxvalue then the linear mapping will have negative gradient.</li>
110 <li><em>thresholdtype</em><br>
111 Either "none", "below", or "above". <em>below</em> and
112 <em>above</em> require an additional <em>threshold value</em> which
113 is used to control the display of features with a score either
114 below or above the value.</li>
120 <p>The remaining lines in the file are the sequence annotation
121 definitions, where the now defined features are attached to regions
122 on particular sequences. Each feature can optionally include some descriptive text
123 which is displayed in a tooltip when the mouse is near the feature on that
124 sequence (and can also be used to generate a colour the feature).</p>
126 <p>If your sequence annotation is already available in GFF Format (see <a href="http://www.sanger.ac.uk/resources/software/gff/spec.html">http://www.sanger.ac.uk/resources/software/gff/spec.html</a>),
127 then you can leave it as is, after first adding a line containing
128 only 'GFF' after any Jalview feature colour definitions (<em>this mixed format capability was added in Jalview 2.6</em>). Alternately, you can use Jalview's own sequence feature
129 annotation format, which additionally allows HTML and URLs to be
130 directly attached to each piece of annotation.</p>
132 <p><strong>Jalview's sequence feature annotation format</strong></p>
134 Each feature is specified as a tab-separated series of columns as defined below:
136 <em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em>	<em>score (optional)</em>
139 This format allows two alternate ways of referring to a sequence, either by
140 its text ID, or its index in an associated alignment. Normally, sequence features are associated with sequences rather
141 than alignments, and the sequenceIndex field is given as "-1". In
142 order to specify a sequence by its index in a particular alignment,
143 the sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the
144 sequenceId field will be used in preference to the sequenceIndex
149 <p>The description may contain simple HTML document body tags if
150 enclosed by "<html></html>" and these will be rendered
151 as formatted tooltips in the Jalview Application (the Jalview
152 applet is not capable of rendering HTML tooltips, so all formatting
153 tags will be removed).<br>
154 <em>Attaching Links to Sequence Features</em><br>
155 Any anchor tags in an html formatted description line will be
156 translated into URL links. A link symbol will be displayed adjacent
157 to any feature which includes links, and these are made available
158 from the <a href="../menus/popupMenu.html#sqid.popup">links
159 submenu</a> of the popup menu which is obtained by right-clicking
160 when a link symbol is displayed in the tooltip.<br>
161 <em>Non-positional features</em><br>
162 Specify the <em>start</em> and <em>end</em> for a feature to be
163 <strong>0</strong> in order to attach it to the whole sequence.
164 Non-positional features are shown in a tooltip when the mouse
165 hovers over the sequence ID panel, and any embedded links can be
166 accessed from the popup menu.<br/> <em>Scores</em><br>
167 Scores can be associated with sequence features, and used to sort
168 sequences or shade the alignment (this was added in jalview 2.5).
169 The score field is optional, and malformed scores will be
172 <p>Feature annotations can be collected into named groups by
173 prefixing definitions with lines of the form:
176 <strong>startgroup groupname</strong>
179 .. and subsequently post-fixing the group with:
182 <strong>endgroup groupname</strong>
185 Feature grouping was introduced in version 2.08, and used to
186 control whether a set of features are either hidden or shown
187 together in the <a href="seqfeatures.html">sequence Feature
188 settings dialog box</a>.</p>
191 <p>A complete example is shown below :
194 metal ion-binding site	00ff00
195 transit peptide	0,105,215
197 modified residue	105,225,35
198 signal peptide	0,155,165
202 Your Own description here	FER_CAPAA	-1	3	93	domain
203 Your Own description here	FER_CAPAN	-1	48	144	chain
204 Your Own description here	FER_CAPAN	-1	50	140	domain
205 Your Own description here	FER_CAPAN	-1	136	136	modified residue
206 Your Own description here	FER1_LYCES	-1	1	47	transit peptide
207 Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
208 Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
209 startgroup	secondarystucture
210 PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
211 PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
212 endgroup	secondarystructure
214 FER_CAPAA	GffGroup	domain	3	93	.	.