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[jalview.git] / help / html / colourSchemes / colourSchemes.html
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
+<html>\r
+<head>\r
+<title>Untitled Document</title>\r
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
+<style type="text/css">\r
+<!--\r
+td {\r
+       text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em><a name="zappo">Zappo Colour</a>s</em><br>\r
+  <br>\r
+  The residues are coloured according to their physico-chemical properties as \r
+  follows: </p>\r
+<div align="center">\r
+  <table width="400" border="1">\r
+    <tr> \r
+      <td > Aliphatic/hydrophobic</td>\r
+      <td bgcolor="#ffafaf">ILVAM </td>\r
+    </tr>\r
+    <tr> \r
+      <td>Aromatic</td>\r
+      <td bgcolor="#ffc800">FWY</td>\r
+    </tr>\r
+    <tr> \r
+      <td>Positive</td>\r
+      <td bgcolor="#6464ff">KRH</td>\r
+    </tr>\r
+    <tr> \r
+      <td> Negative</td>\r
+      <td bgcolor="#ff0000">DE</td>\r
+    </tr>\r
+    <tr> \r
+      <td>Hydrophilic</td>\r
+      <td bgcolor="#00ff00">STNQ</td>\r
+    </tr>\r
+    <tr> \r
+      <td>conformationally special</td>\r
+      <td bgcolor="#ff00ff">PG</td>\r
+    </tr>\r
+    <tr> \r
+      <td>Cysteine</td>\r
+      <td bgcolor="#ffff00">C</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center"></p>\r
+<p><em><a name="taylor">Taylor</a></em></p>\r
+<p>These colours were invented by Willie Taylor and an entertaining description \r
+  of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>\r
+<div align="center">\r
+  <table width="400" border="1">\r
+    <tr> \r
+      <td bgcolor="#ccff00">A</td>\r
+      <td bgcolor="#99ff00">V</td>\r
+      <td bgcolor="#66ff00">I</td>\r
+      <td bgcolor="#33ff00">L</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#00ff00">M</td>\r
+      <td bgcolor="#00ff66">F</td>\r
+      <td bgcolor="#00ffcc">Y</td>\r
+      <td bgcolor="#00ccff">W</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#0066ff">H</td>\r
+      <td bgcolor="#0000ff">R</td>\r
+      <td bgcolor="#6600ff">K</td>\r
+      <td bgcolor="#cc00ff">N</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#ff00cc">Q</td>\r
+      <td bgcolor="#ff0066">E</td>\r
+      <td bgcolor="#ff0000">D</td>\r
+      <td bgcolor="#ff3300">S</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#ff6600">T</td>\r
+      <td bgcolor="#ff9900">G</td>\r
+      <td bgcolor="#ffcc00">P</td>\r
+      <td bgcolor="#ffff00">C</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center">&nbsp;</p>\r
+<p><em><a name="hydrophobic">Hydrophobicity</a></em></p>\r
+<p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J. \r
+  Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this \r
+  table are coloured red and the most hydrophilic ones are coloured blue.</p>\r
+<div align="center">\r
+  <table width="400" border="1">\r
+    <tr> \r
+      <td bgcolor="#ff0000">I</td>\r
+      <td bgcolor="#f60009">V</td>\r
+      <td bgcolor="#ea0015">L</td>\r
+      <td bgcolor="#cb0034">F</td>\r
+      <td bgcolor="#c2003d">C</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#b0004f">M</td>\r
+      <td bgcolor="#ad0052">A</td>\r
+      <td bgcolor="#6a0095">G</td>\r
+      <td bgcolor="#680097">X</td>\r
+      <td bgcolor="#61009e">T</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#5e00a1">S</td>\r
+      <td bgcolor="#5b00a4">W</td>\r
+      <td bgcolor="#4f00b0">Y</td>\r
+      <td bgcolor="#4600b9">P</td>\r
+      <td bgcolor="#1500ea">H</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#0c00f3">E</td>\r
+      <td bgcolor="#0c00f3">Z</td>\r
+      <td bgcolor="#0c00f3">Q</td>\r
+      <td bgcolor="#0c00f3">D</td>\r
+      <td bgcolor="#0c00f3">B</td>\r
+    </tr>\r
+    <tr> </td>\r
+      <td bgcolor="#0c00f3">N</td>\r
+      <td bgcolor="#0000ff">K</td>\r
+      <td bgcolor="#0000ff">R</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center">&nbsp;</p>\r
+<p><em><a name="helix">Helix Propensity</a></em></p>\r
+<div align="center">\r
+  <table width="400" border="1">\r
+    <tr> \r
+      <td bgcolor="#ff00ff">E</td>\r
+      <td bgcolor="#ef10ef">M</td>\r
+      <td bgcolor="#e718e7">A</td>\r
+      <td bgcolor="#c936c9">Z</td>\r
+      <td bgcolor="#ae51ae">L</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#a05fa0">K</td>\r
+      <td bgcolor="#986798">F</td>\r
+      <td bgcolor="#926d92">Q</td>\r
+      <td bgcolor="#8a758a">I</td>\r
+      <td bgcolor="#8a758a">W</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#857a85">V</td>\r
+      <td bgcolor="#778877">D</td>\r
+      <td bgcolor="#758a75">X</td>\r
+      <td bgcolor="#758a75">H</td>\r
+      <td bgcolor="#6f906f">R</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#49b649">B</td>\r
+      <td bgcolor="#47b847">T</td>\r
+      <td bgcolor="#36c936">S</td>\r
+      <td bgcolor="#23dc23">C</td>\r
+      <td bgcolor="#21de21">Y</td>\r
+    </tr>\r
+    <tr> </td>\r
+      <td bgcolor="#1be41b">N</td>\r
+      <td bgcolor="#00ff00">G</td>\r
+      <td bgcolor="#00ff00">P</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center">&nbsp;</p>\r
+<p><em><a name="strand">Strand propensity</a></em></p>\r
+<div align="center">\r
+  <table width="400" border="1">\r
+    <tr> \r
+      <td bgcolor="#ffff00">V</td>\r
+      <td bgcolor="#ecec13">I</td>\r
+      <td bgcolor="#d3d32c">Y</td>\r
+      <td bgcolor="#c2c23d">F</td>\r
+      <td bgcolor="#c0c03f">W</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#b2b24d">L</td>\r
+      <td bgcolor="#9d9d62">T</td>\r
+      <td bgcolor="#9d9d62">C</td>\r
+      <td bgcolor="#8c8c73">Q</td>\r
+      <td bgcolor="#82827d">M</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#797986">X</td>\r
+      <td bgcolor="#6b6b94">R</td>\r
+      <td bgcolor="#64649b">N</td>\r
+      <td bgcolor="#60609f">H</td>\r
+      <td bgcolor="#5858a7">A</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#4949b6">S</td>\r
+      <td bgcolor="#4949b6">G</td>\r
+      <td bgcolor="#4747b8">Z</td>\r
+      <td bgcolor="#4747b8">K</td>\r
+      <td bgcolor="#4343bc">B</td>\r
+    </tr>\r
+    <tr> </td>\r
+      <td bgcolor="#2323dc">P</td>\r
+      <td bgcolor="#2121de">D</td>\r
+      <td bgcolor="#0000ff">E</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center">&nbsp;</p>\r
+<p><em><a name="turn">Turn propensity</a></em></p>\r
+<div align="center">\r
+  <table width="400" border="1">\r
+    <tr> \r
+      <td bgcolor="#ff0000">N</td>\r
+      <td bgcolor="#ff0000">G</td>\r
+      <td bgcolor="#f60909">P</td>\r
+      <td bgcolor="#f30c0c">B</td>\r
+      <td bgcolor="#e81717">D</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#e11e1e">S</td>\r
+      <td bgcolor="#a85757">C</td>\r
+      <td bgcolor="#9d6262">Y</td>\r
+      <td bgcolor="#7e8181">K</td>\r
+      <td bgcolor="#7c8383">X</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#778888">Q</td>\r
+      <td bgcolor="#738c8c">W</td>\r
+      <td bgcolor="#738c8c">T</td>\r
+      <td bgcolor="#708f8f">R</td>\r
+      <td bgcolor="#708f8f">H</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#5ba4a4">Z</td>\r
+      <td bgcolor="#3fc0c0">E</td>\r
+      <td bgcolor="#2cd3d3">A</td>\r
+      <td bgcolor="#1ee1e1">F</td>\r
+      <td bgcolor="#1ee1e1">M</td>\r
+    </tr>\r
+    <tr> </td>\r
+      <td bgcolor="#1ce3e3">L</td>\r
+      <td bgcolor="#07f8f8">V</td>\r
+      <td bgcolor="#00ffff">I</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center">&nbsp;</p>\r
+<p><em><a name="buried"></a>Buried index</a></em></p>\r
+<div align="center">\r
+  <table width="400" border="1">\r
+    <tr> \r
+      <td bgcolor="#0000ff">C</td>\r
+      <td bgcolor="#0054ab">I</td>\r
+      <td bgcolor="#005fa0">V</td>\r
+      <td bgcolor="#007b84">L</td>\r
+      <td bgcolor="#008778">F</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#009768">M</td>\r
+      <td bgcolor="#009d62">G</td>\r
+      <td bgcolor="#00a35c">A</td>\r
+      <td bgcolor="#00a857">W</td>\r
+      <td bgcolor="#00b649">X</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#00d52a">S</td>\r
+      <td bgcolor="#00d52a">H</td>\r
+      <td bgcolor="#00db24">T</td>\r
+      <td bgcolor="#00e01f">P</td>\r
+      <td bgcolor="#00e619">Y</td>\r
+    </tr>\r
+    <tr> \r
+      <td bgcolor="#00eb14">N</td>\r
+      <td bgcolor="#00eb14">B</td>\r
+      <td bgcolor="#00eb14">D</td>\r
+      <td bgcolor="#00f10e">Q</td>\r
+      <td bgcolor="#00f10e">Z</td>\r
+    </tr>\r
+    <tr> </td>\r
+      <td bgcolor="#00f10e">E</td>\r
+      <td bgcolor="#00fc03">R</td>\r
+      <td bgcolor="#00ff00">K</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center">&nbsp;</p>\r
+<p><em></em><a name="nucleotide">Nucleotide Colours</a></em></p>\r
+<div align="center">\r
+  <table width="200" border="1">\r
+    <tr> \r
+      <td bgcolor="#64F73F">A</td>\r
+      <td bgcolor="#FFB340">C</td>\r
+      <td bgcolor="#EB413C">G</td>\r
+      <td bgcolor="#3C88EE">T</td>\r
+    </tr>\r
+  </table>\r
+</div>\r
+<p align="center">&nbsp;</p>\r
+<p><em><a name="blosum"></a>Blosum62</a></em></p>\r
+<p>Gaps are coloured white. If a residue matchs the consensus sequence residue \r
+  at that position it is colored dark blue. If it does not match the consensus \r
+  residue but the 2 residues have a positive Blosum62 score, it is colored light \r
+  blue.</p>\r
+<p>&nbsp;</p>\r
+<p><em><a name="pid">Colouring above a percentage identity threshold</a></em><br>\r
+  Selecting this option causes the colour scheme to be applied to only those residues \r
+  that occur in that column more than a certain percentage of the time. For instance \r
+  selecting the threshold to be 100 will only colour those columns with 100 % \r
+  identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity \r
+  and User colour schemes. <br>\r
+  This option depends on a consensus calculation having been performed. If no \r
+  consensus exists (e.g. after a copy or a clustalw alignment) then no residues \r
+  are coloured.</p>\r
+<p><em>PID Colours</em><br>\r
+  This depends on the applet having performed a consensus calculation on the alignment.<br>\r
+  The PID option colours the residues (boxes and/or text) according to the percentage \r
+  of the residues in each column that agree with the consensus sequence. Only \r
+  the residues that agree with the consensus residue for each column are coloured.<br>\r
+</p>\r
+<p>&nbsp;</p>\r
+<p> </p>\r
+</body>\r
+</html>\r