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: {&gt;X%,xx,y},
  44     where X is the threshold percentage presence for any of the xx (or y)
  45     residue types.
  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>
  47   <div align="center">
  48     <p>&nbsp;</p>
  49     <table border="1">
  50       <tr>
  51         <th>Clustal X Default Colouring</th>
  52       </tr>
  53       <tr>
  54         <td><table border="1">
  55             <tr>
  56               <th>Category</th>
  57               <th>Colour</th>
  58               <th>Residue at position</th>
  59               <th>{ Threshold, Residue group }</th>
  60             </tr>
  61             <tr>
  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>{&gt;60%, WLVIMAFCHP}</td>
  66             </tr>
  67             <tr>
  68               <td>C</td>
  69               <td>{&gt;60%, WLVIMAFCHP}</td>
  70             </tr>
  71             <tr>
  72               <td>Positive charge</td>
  73               <td bgcolor="#f01505">RED</td>
  74               <td>K,R</td>
  75               <td>{&gt;60%,KR},{&gt;80%, K,R,Q}</td>
  76             </tr>
  77             <tr>
  78               <td rowspan="2">Negative charge</td>
  79               <td rowspan="2" bgcolor="#c048c0">MAGENTA</td>
  80               <td>E</td>
  81               <td>{&gt;60%,KR},{&gt;50%,QE},{&gt;85%,E,Q,D}</td>
  82             </tr>
  83             <tr>
  84               <td>D</td>
  85               <td>{&gt;60%,KR}, {&gt;85%, K,R,Q}, {&gt;50%,ED}</td>
  86             </tr>
  87             <tr>
  88               <td rowspan="3">Polar</td>
  89               <td rowspan="3" bgcolor="#15c015">GREEN</td>
  90               <td>N</td>
  91               <td>{&gt;50%, N}, {&gt;85%, N,Y}</td>
  92             </tr>
  93             <tr>
  94               <td>Q</td>
  95               <td>{&gt;60%,KR},{&gt;50%,QE},{&gt;85%,Q,E,K,R}</td>
  96             </tr>
  97             <tr>
  98               <td>S,T</td>
  99               <td>{&gt;60%, WLVIMAFCHP}, {&gt;50%, TS}, {&gt;85%,S,T}</td>
 100             </tr>
 101             <tr>
 102               <td>Cysteines</td>
 103               <td bgcolor="#f08080">PINK</td>
 104               <td>C</td>
 105               <td>{>85%, C}</td>
 106             </tr>
 107             <tr>
 108               <td>Glycines</td>
 109               <td bgcolor="#f09048">ORANGE</td>
 110               <td>G</td>
 111               <td>{&gt;0%, G}</td>
 112             </tr>
 113             <tr>
 114               <td>Prolines</td>
 115               <td bgcolor="#c0c000">YELLOW</td>
 116               <td>P</td>
 117               <td>{&gt;0%, P}</td>
 118             </tr>
 119             <tr>
 120               <td>Aromatic</td>
 121               <td bgcolor="#15a4a4">CYAN</td>
 122               <td>H,Y</td>
 123               <td>{&gt;60%, WLVIMAFCHP}, {&gt;85%,
 124                 W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
 125             </tr>
 126             <tr>
 127               <td>Unconserved</td>
 128               <td>WHITE</td>
 129               <td>any / gap</td>
 130               <td>If none of the above criteria are met</td>
 131             </tr>
 132           </table></td>
 133       </tr>
 134     </table>
 135   </div>
 136 </body>
 137 </html>