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[jalview.git] / help / html / colourSchemes / clustal.html
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22 <head>
23 <title>Clustal Colour Scheme</title>
24 <style type="text/css">
25 <!--
26 td {
27         text-align: center;
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30 </style>
31 </head>
32
33 <body>
34   <p>
35     <strong>Clustal X Colour Scheme</strong>
36   </p>
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
42     type.</p>
43   <p>The table below gives these criteria as clauses: {+X%,xx,y},
44     where X is the minimum percentage presence for any of the xx (or y)
45     residue types.</p>
46   <div align="center">
47     <p>&nbsp;</p>
48     <table border="1">
49       <tr>
50         <th>Clustal X Default Colouring</th>
51       </tr>
52       <tr>
53         <td><table border="1">
54             <tr>
55               <th>Residue at position</th>
56               <th>Applied Colour</th>
57               <th>{ Threshhold, Residue group }</th>
58             </tr>
59             <tr>
60               <td>A,I,L,M,F,W,V</td>
61               <td bgcolor="#80a0f0">BLUE</td>
62               <td>{+60%, WLVIMAFCHP}</td>
63             </tr>
64             <tr>
65               <td>R,K</td>
66               <td bgcolor="#f01505">RED</td>
67               <td>{+60%,KR},{+80%, K,R,Q}</td>
68             </tr>
69             <tr>
70               <td>N</td>
71               <td bgcolor="#15c015">GREEN</td>
72               <td>{+50%, N}, {+85%, N,Y}</td>
73             </tr>
74             <tr>
75               <td>C</td>
76               <td bgcolor="#80a0f0">BLUE</td>
77               <td>{+60%, WLVIMAFCHP}</td>
78             </tr>
79             <tr>
80               <td>C</td>
81               <td bgcolor="#f08080">PINK</td>
82               <td>{100%, C}</td>
83             </tr>
84             <tr>
85               <td>Q</td>
86               <td bgcolor="#15c015">GREEN</td>
87               <td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td>
88             </tr>
89             <tr>
90               <td>E</td>
91               <td bgcolor="#c048c0">MAGENTA</td>
92               <td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td>
93             </tr>
94             <tr>
95               <td>D</td>
96               <td bgcolor="#c048c0">MAGENTA</td>
97               <td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td>
98             </tr>
99             <tr>
100               <td>G</td>
101               <td bgcolor="#f09048">ORANGE</td>
102               <td>{+0%, G}</td>
103             </tr>
104             <tr>
105               <td>H,Y</td>
106               <td bgcolor="#15a4a4">CYAN</td>
107               <td>{+60%, WLVIMAFCHP}, {+85%,
108                 W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
109             </tr>
110             <tr>
111               <td>P</td>
112               <td bgcolor="#c0c000">YELLOW</td>
113               <td>{+0%, P}</td>
114             </tr>
115             <tr>
116               <td>S,T</td>
117               <td bgcolor="#15c015">GREEN</td>
118               <td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td>
119             </tr>
120           </table></td>
121       </tr>
122     </table>
123   </div>
124 </body>
125 </html>