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23 <title>Clustal Colour Scheme</title>
24 <style type="text/css">
35 <strong>Clustal X Colour Scheme</strong>
37 <p>This is an emulation of the default colourscheme used for
38 alignments in Clustal X, a graphical interface for the ClustalW
39 multiple sequence alignment program. Each residue in the alignment
40 is assigned a colour if the amino acid profile of the alignment at
41 that position meets some minimum criteria specific for the residue
43 <p>The table below gives these criteria as clauses: {>X%,xx,y},
44 where X is the threshold percentage presence for any of the xx (or y)
46 <br>For example, K or R is coloured red if the column includes more than 60% K or R (combined), or more than 80% of either K or R or Q (individually).</p>
51 <th>Clustal X Default Colouring</th>
54 <td><table border="1">
58 <th>Residue at position</th>
59 <th>{ Threshold, Residue group }</th>
62 <td rowspan="2">Hydrophobic</td>
63 <td rowspan="2" bgcolor="#80a0f0">BLUE</td>
64 <td>A,I,L,M,F,W,V</td>
65 <td>{>60%, WLVIMAFCHP}</td>
69 <td>{>60%, WLVIMAFCHP}</td>
72 <td>Positive charge</td>
73 <td bgcolor="#f01505">RED</td>
75 <td>{>60%,KR},{>80%, K,R,Q}</td>
78 <td rowspan="2">Negative charge</td>
79 <td rowspan="2" bgcolor="#c048c0">MAGENTA</td>
81 <td>{>60%,KR},{>50%,QE},{>85%,E,Q,D}</td>
85 <td>{>60%,KR}, {>85%, K,R,Q}, {>50%,ED}</td>
88 <td rowspan="3">Polar</td>
89 <td rowspan="3" bgcolor="#15c015">GREEN</td>
91 <td>{>50%, N}, {>85%, N,Y}</td>
95 <td>{>60%,KR},{>50%,QE},{>85%,Q,E,K,R}</td>
99 <td>{>60%, WLVIMAFCHP}, {>50%, TS}, {>85%,S,T}</td>
103 <td bgcolor="#f08080">PINK</td>
109 <td bgcolor="#f09048">ORANGE</td>
115 <td bgcolor="#c0c000">YELLOW</td>
121 <td bgcolor="#15a4a4">CYAN</td>
123 <td>{>60%, WLVIMAFCHP}, {>85%,
124 W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
130 <td>If none of the above criteria are met</td>