help/html/colourSchemes/clustal.html

   1 <html>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  -->
  22 <head>
  23 <title>Clustal Colour Scheme</title>
  24 <style type="text/css">
  25 <!--
  26 td {
  27         text-align: center;
  28 }
  29 -->
  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>