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23 <meta name="generator" content="HTML Tidy, see www.w3.org">
24 <title>Sequence Features File</title>
28 <strong>Sequence Features File</strong>
30 <p>The Sequence features file (which used to be known as the
31 "Groups file" prior to version 2.08) is a simple way of getting your
32 own sequence annotations into Jalview. It was introduced to allow
33 sequence features to be rendered in the Jalview applet, and so is
34 intentionally lightweight and minimal because the applet is often
35 used in situations where data file size must be kept to a minimum,
36 and no XML parser is available.</p>
39 Features files are imported into Jalview in the following ways:<br>
41 <li>from the command line <pre>
42 <strong> -features <<em>Features filename</em>></strong>
46 <li>Dragging a features file onto an alignment window</li>
48 <li>Via the "Load Features / Annotations" entry in
49 the <strong>File</strong> menu of an alignment window.
56 <strong>Sequence Features File Format</strong>
59 A features file is a simple ASCII text file, where each line
60 contains tab separated text fields. <strong>No comments are
63 <p>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 can
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: <pre>
79 [label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
80 </pre> The fields are as follows:
83 <li><em>label</em><br> Indicate that the feature
84 description should be used to create a colour for features of
85 this type.<br> <em>Note: if no threshold value is
86 needed then the final '|' may be omitted.<br> This
87 keyword was added in Jalview 2.6
90 <li><em>mincolor</em> and <em>maxcolor</em><br> Colour
91 triplets specified as hexadecimal or comma separated values
92 (may be left blank for a <em>label</em> style colourscheme,
93 but remember to specify the remaining fields)</li>
95 <li><em>absolute</em><br> An optional switch
96 indicating that the <em>minvalue</em> and <em>maxvalue</em>
97 parameters should be left as is, rather than rescaled
98 according to the range of scores for this feature type.</li>
100 <li><em>minvalue</em> and <em>maxvalue</em><br>
101 Minimum and maximum values defining the range of scores for
102 which the colour range will be defined over. If minvalue is
103 greater than maxvalue then the linear mapping will have
104 negative gradient.</li>
106 <li><em>thresholdtype</em><br> Either
107 "none", "below", or "above". <em>below</em>
108 and <em>above</em> require an additional <em>threshold
109 value</em> which is used to control the display of features with
110 a score either below or above the value.</li>
116 <p>The remaining lines in the file are the sequence annotation
117 definitions, where the now defined features are attached to regions
118 on particular sequences. Each feature can optionally include some
119 descriptive text which is displayed in a tooltip when the mouse is
120 near the feature on that sequence (and can also be used to generate
121 a colour the feature).</p>
124 If your sequence annotation is already available in GFF Format (see
125 <a href="http://gmod.org/wiki/GFF2">gmod.org/wiki/GFF2</a>),
126 then you can leave it as is, after first adding a line containing
127 only 'GFF' after any Jalview feature colour definitions (<em>this
128 mixed format capability was added in Jalview 2.6</em>). Alternately,
129 you can use Jalview's own sequence feature annotation format, which
130 additionally allows HTML and URLs to be directly attached to each
135 <strong>Jalview's sequence feature annotation format</strong>
137 <p>Each feature is specified as a tab-separated series of columns
140 <em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em>	<em>score (optional)</em>
143 This format allows two alternate ways of referring to a sequence,
144 either by its text ID, or its index (base 0) in an associated alignment.
145 Normally, sequence features are associated with sequences rather than
146 alignments, and the sequenceIndex field is given as "-1". In
147 order to specify a sequence by its index in a particular alignment,
148 the sequenceId should be given as "ID_NOT_SPECIFIED",
149 otherwise the sequenceId field will be used in preference to the
155 The description may contain simple HTML document body tags if
156 enclosed by "<html></html>" and these will be
157 rendered as formatted tooltips in the Jalview Application (the
158 Jalview applet is not capable of rendering HTML tooltips, so all
159 formatting tags will be removed).<br> <em>Attaching Links
160 to Sequence Features</em><br> Any anchor tags in an html formatted
161 description line will be translated into URL links. A link symbol
162 will be displayed adjacent to any feature which includes links, and
163 these are made available from the <a
164 href="../menus/popupMenu.html#sqid.popup"
165 >links submenu</a> of the popup menu which is obtained by
166 right-clicking when a link symbol is displayed in the tooltip.<br>
167 <em>Non-positional features</em><br> Specify the <em>start</em>
168 and <em>end</em> for a feature to be <strong>0</strong> in order to
169 attach it to the whole sequence. Non-positional features are shown
170 in a tooltip when the mouse hovers over the sequence ID panel, and
171 any embedded links can be accessed from the popup menu.<br /> <em>Scores</em><br>
172 Scores can be associated with sequence features, and used to sort
173 sequences or shade the alignment (this was added in Jalview 2.5).
174 The score field is optional, and malformed scores will be ignored.
177 <p>Feature annotations can be collected into named groups by
178 prefixing definitions with lines of the form:
180 <strong>startgroup groupname</strong>
183 .. and subsequently post-fixing the group with:
186 <strong>endgroup groupname</strong>
189 Feature grouping was introduced in version 2.08, and used to control
190 whether a set of features are either hidden or shown together in the
191 <a href="seqfeatures.html">sequence Feature settings dialog box</a>.
195 <p>A complete example is shown below :
198 metal ion-binding site	00ff00
199 transit peptide	0,105,215
201 modified residue	105,225,35
202 signal peptide	0,155,165
206 Your Own description here	FER_CAPAA	-1	3	93	domain
207 Your Own description here	FER_CAPAN	-1	48	144	chain
208 Your Own description here	FER_CAPAN	-1	50	140	domain
209 Your Own description here	FER_CAPAN	-1	136	136	modified residue
210 Your Own description here	FER1_LYCES	-1	1	47	transit peptide
211 Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
212 Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
213 startgroup	secondarystucture
214 PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
215 PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
216 endgroup	secondarystructure
218 FER_CAPAA	GffGroup	domain	3	93	.	.