4 <title>Sequence Features File</title>
8 <p><strong>Sequence Features File</strong></p>
9 <p>The Sequence features file (which used to be known as the
10 "Groups file" prior to version 2.08) is a simple way of
11 getting your own sequence annotations into Jalview. It was introduced to
12 allow sequence features to be rendered in the Jalview applet, and so is
13 intentionally lightweight and minimal because the applet is often used
14 in situations where data file size must be kept to a minimum, and no XML
15 parser is available.</p>
16 <p>Features files are imported into Jalview in the following ways:<br>
18 <li>from the command line<strong><pre>
19 -features <<em>Features filename</em>></pre></strong></li>
20 <li>Dragging a features file onto an alignment window</li>
21 <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
22 menu of an alignment window.</li>
25 <p><strong>Sequence Features File Format</strong></p>
26 <p>A features file is a simple ASCII text file, where each line
27 contains tab separated text fields. <strong>No comments are
29 <p>The first set of lines contain type definitions:<strong>
30 <pre><em>Feature label</em>	<em>Feature Colour</em></pre> </strong>A feature
31 type has a text label, and a colour (specified as a red,green,blue 24
32 bit triplet either in hexadecimal (eg. 00ff00) or as comma separated
33 numbers (ranging from 0 to 255)). The text label may contain simple HTML
34 document body tags if enclosed by "<html></html>"
35 and will be rendered as formatted tooltips in the Jalview Application
36 (the Jalview applet is not capable of rendering HTML tooltips, so all
37 formatting tags will be removed.</p>
38 <p>The remaining lines in the file are the sequence annotation
39 definitions, where the now defined features are attached to regions on
40 particular sequences, optionally with some descriptive text (displayed
41 in a tooltip when the mouse is near the feature on that sequence). There
42 are two alternate ways of referring to a sequence, either by its text
43 ID, or its index in an associated alignment.
45 <em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em></pre>
46 Normally, sequence features are associated with sequences rather than
47 alignments, and the sequenceIndex field is given as "-1". In
48 order to specify a sequence by its index in a particular alignment, the
49 sequenceId should be given as "ID_NOT_SPECIFIED", otherwise
50 the sequenceId field will be used in preference to the sequenceIndex
53 <p>Feature annotations can be collected into named groups by
54 prefixing definitions with lines of the form:<strong><pre>startgroup	groupname</pre></strong>..
55 and subsequently post-fixing the group with:<strong><pre>endgroup	groupname</pre></strong>Feature
56 grouping was introduced in version 2.08, and used to control whether a
57 set of features are either hidden or shown together in the <a
58 href="seqfeatures.html">sequence Feature settings dialog box</a>.</p>
59 <p>A complete example is shown below :
62 metal ion-binding site	00ff00
63 transit peptide	0,105,215
65 modified residue	105,225,35
66 signal peptide	0,155,165
70 Your Own description here	FER_CAPAA	-1	3	93	domain
71 Your Own description here	FER_CAPAN	-1	48	144	chain
72 Your Own description here	FER_CAPAN	-1	50	140	domain
73 Your Own description here	FER_CAPAN	-1	136	136	modified residue
74 Your Own description here	FER1_LYCES	-1	1	47	transit peptide
75 Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
76 Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
77 startgroup	secondarystucture
78 PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
79 PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
80 endgroup	secondarystructure
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