3 <head><title>Sequence Features File</title></head>
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6 <p><strong>Sequence Features File</strong></p>
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7 <p>The Sequence features file (which used to be known as the "Groups
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8 file" prior to version 2.08) is a simple way of getting
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9 your own sequence annotations into Jalview. It was introduced to allow
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10 sequence features to be rendered in the Jalview applet, and so is
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11 intentionally lightweight and minimal because the applet is often used
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12 in situations where data file size must be kept to a minimum, and no
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13 XML parser is available.</p>
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14 <p>Features files are imported into Jalview in the following ways:<br>
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16 <li>from the command line<strong><pre>
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17 -features <<em>Features filename</em>></pre></strong></li>
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18 <li>Dragging a features file onto an alignment window</li>
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19 <li>Via the "Load Features / Annotations" entry in the
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20 <strong>File</strong> menu of an alignment window.</li>
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23 <p><strong>Sequence Features File Format</strong></p>
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24 <p>A features file is a simple ASCII text file, where each line
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25 contains tab separated text fields. <strong>No comments are
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26 allowed</strong>.</p>
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27 <p>The first set of lines contain type definitions:<strong>
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28 <pre><em>Feature label</em>	<em>Feature Colour</em></pre>
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29 </strong>A feature type has a text label, and a colour (specified as a
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30 red,green,blue 24 bit triplet either in hexadecimal (eg. 00ff00) or as comma
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31 separated numbers (ranging from 0 to 255)).
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32 <p>The remaining lines in the file are the sequence annotation
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33 definitions, where the now defined features are attached to regions on
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34 particular sequences, optionally with some descriptive text (displayed
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35 in a tooltip when the mouse is near the feature on that sequence). There are two alternate ways of referring to a
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36 sequence, either by its text ID, or its index in an associated
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38 <em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em></pre>Normally,
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39 sequence features are associated with sequences rather than
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40 alignments, and the sequenceIndex field is given as "-1". In
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41 order to specify a sequence by its index in a particular alignment, the
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42 sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the
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43 sequenceId field will be used in preference to the sequenceIndex field.</p><p>
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44 Feature annotations can be collected into named groups by prefixing
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45 definitions with lines of the
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46 form:<strong><pre>startgroup	groupname</pre></strong>.. and
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47 subsequently post-fixing the group
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48 with:<strong><pre>endgroup	groupname</pre></strong>Feature grouping
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49 was introduced in version 2.08, and used to control whether a set of features
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50 are either hidden or shown together in the <a href="seqfeatures.html">sequence Feature settings
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52 <p>A complete example is shown below :<pre>
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54 metal ion-binding site	00ff00
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55 transit peptide	0,105,215
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57 modified residue	105,225,35
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58 signal peptide	0,155,165
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62 Your Own description here	FER_CAPAA	-1	3	93	domain
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63 Your Own description here	FER_CAPAN	-1	48	144	chain
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64 Your Own description here	FER_CAPAN	-1	50	140	domain
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65 Your Own description here	FER_CAPAN	-1	136	136	modified residue
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66 Your Own description here	FER1_LYCES	-1	1	47	transit peptide
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67 Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
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68 Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
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69 startgroup	secondarystucture
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70 PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
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71 PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
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72 endgroup	secondarystructure
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