2 <head><title>Clustal Colour Scheme</title>
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3 <style type="text/css">
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13 <p><em>Clustal X Colour Scheme</em></p>
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14 <p>This is an emulation of the default colourscheme used for alignments in
15 Clustal X, a graphical interface for the ClustalW multiple sequence alignment
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16 program. Each residue in the alignment is assigned a colour if the
17 amino acid profile of the alignment at that position
18 meets some minimum criteria specific for the residue type.</p>
19 <p>The table below gives these criteria as clauses: {+X%,xx,y},
20 where X is the minimum percentage presence for any of the xx (or y) residue types.</p>
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21 <div align="center">
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22 <p> </p><table border="1">
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23 <tr><th>Clustal X Default Colouring</th></tr>
25 <td><table border="1">
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26 <tr><th>Residue at position</th><th>Applied Colour</th><th>{ Threshhold, Residue group }</th></tr>
27 <tr><td>A,I,L,M,F,W,V</td><td bgcolor="#80a0f0">BLUE</td><td>{+60%, WLVIMAFCHP}</td></tr>
28 <tr><td>R,K</td><td bgcolor="#f01505">RED</td><td>{+60%,KR},{+80%, K,R,Q}</td></tr>
29 <tr><td>N</td><td bgcolor="#15c015">GREEN</td><td>{+50%, N}, {+85%, N,Y}</td></tr>
30 <tr><td>C</td><td bgcolor="#80a0f0">BLUE</td>
31 <td>{+60%, WLVIMAFCHP}</td></tr>
32 <tr><td>C</td><td bgcolor="#f08080">PINK</td>
33 <td>{100%, C}</td></tr>
34 <tr><td>Q</td><td bgcolor="#15c015">GREEN</td><td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td></tr>
35 <tr><td>E</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td></tr>
36 <tr><td>D</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td></tr>
37 <tr><td>G</td><td bgcolor="#f09048">ORANGE</td><td>{+0%, G}</td></tr>
38 <tr><td>H,Y</td><td bgcolor="#15a4a4">CYAN</td><td>{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}</td></tr>
39 <tr><td>P</td><td bgcolor="#c0c000">YELLOW</td><td>{+0%, P}</td></tr>
40 <tr><td>S,T</td><td bgcolor="#15c015">GREEN</td><td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td></tr>