help/html/colourSchemes/index.html

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  22 <head>
  23 <title>Colour Schemes</title>
  24 <style type="text/css">
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  33 </head>
  34 <body>
  35 <p><strong>Colour schemes</strong></p>
  36 <p>Jalview allows the user to set a background colour for the whole
  37 alignment view or for each group defined on regions within it.</p>
  38 <p>To change the background colour, simply select the colour from
  39 the &quot;Colour&quot; menu.</p>
  40 <p>To change the colour of a group, right click on any residue
  41 within a group and use the popup menu to define the group colour.</p>
  42 <p>At the top of the &quot;Colour&quot; menu the tick box
  43 &quot;Apply Background Colour to all groups&quot;. This is ticked by
  44 default so that a chosen colour scheme will be applied to all existing
  45 groups. If you wish to maintain the colour scheme for defined groups,
  46 make sure you deselect this option before changing the background
  47 colour.</p>
  48 <p>The <strong>&quot;Colour&#8594;<a
  49         href="../colourSchemes/textcolour.html">Colour Text...</a>&quot;</strong> entry
  50 opens a dialog box to set a different text colour for light and dark
  51 background, and the intensity threshold for transition between them.</p>
  52 <p>The default colour schemes are summarised in the table below:
  53 <div align="center">
  54 <p>&nbsp;</p>
  55 <p><strong>Protein Colour Schemes</strong></p>
  56 <table border="1">
  57         <tr>
  58                 <td>
  59                 <table border="1">
  60                         <tr>
  61                                 <td nowrap></td>
  62                                 <td>A</td>
  63                                 <td>R</td>
  64                                 <td>N</td>
  65                                 <td>D</td>
  66                                 <td>C</td>
  67                                 <td>Q</td>
  68                                 <td>E</td>
  69                                 <td>G</td>
  70                                 <td>H</td>
  71                                 <td>I</td>
  72                                 <td>L</td>
  73                                 <td>K</td>
  74                                 <td>M</td>
  75                                 <td>F</td>
  76                                 <td>P</td>
  77                                 <td>S</td>
  78                                 <td>T</td>
  79                                 <td>W</td>
  80                                 <td>Y</td>
  81                                 <td>V</td>
  82                                 <td>B</td>
  83                                 <td>X</td>
  84                                 <td>Z</td>
  85                         </tr>
  86                         <tr>
  87                                 <td height="24">Clustal</td>
  88                                 <td bgcolor="#80a0f0"></td>
  89                                 <td bgcolor="#f01505"></td>
  90                                 <td bgcolor="#00ff00"></td>
  91                                 <td bgcolor="#c048c0"></td>
  92                                 <td bgcolor="#f08080"></td>
  93                                 <td bgcolor="#00ff00"></td>
  94                                 <td bgcolor="#c048c0"></td>
  95                                 <td bgcolor="#f09048"></td>
  96                                 <td bgcolor="#15a4a4"></td>
  97                                 <td bgcolor="#80a0f0"></td>
  98                                 <td bgcolor="#80a0f0"></td>
  99                                 <td bgcolor="#f01505"></td>
 100                                 <td bgcolor="#80a0f0"></td>
 101                                 <td bgcolor="#80a0f0"></td>
 102                                 <td bgcolor="#ffff00"></td>
 103                                 <td bgcolor="#00ff00"></td>
 104                                 <td bgcolor="#00ff00"></td>
 105                                 <td bgcolor="#80a0f0"></td>
 106                                 <td bgcolor="#15a4a4"></td>
 107                                 <td bgcolor="#80a0f0"></td>
 108                                 <td></td>
 109                                 <td></td>
 110                                 <td></td>
 111                         </tr>
 112                         <tr>
 113                                 <td height="24">Zappo</td>
 114                                 <td bgcolor="#ffafaf"></td>
 115                                 <td bgcolor="#6464ff"></td>
 116                                 <td bgcolor="#00ff00"></td>
 117                                 <td bgcolor="#ff0000"></td>
 118                                 <td bgcolor="#ffff00"></td>
 119                                 <td bgcolor="#00ff00"></td>
 120                                 <td bgcolor="#ff0000"></td>
 121                                 <td bgcolor="#ff00ff"></td>
 122                                 <td bgcolor="#6464ff"></td>
 123                                 <td bgcolor="#ffafaf"></td>
 124                                 <td bgcolor="#ffafaf"></td>
 125                                 <td bgcolor="#6464ff"></td>
 126                                 <td bgcolor="#ffafaf"></td>
 127                                 <td bgcolor="#ffc800"></td>
 128                                 <td bgcolor="#ff00ff"></td>
 129                                 <td bgcolor="#00ff00"></td>
 130                                 <td bgcolor="#00ff00"></td>
 131                                 <td bgcolor="#ffc800"></td>
 132                                 <td bgcolor="#ffc800"></td>
 133                                 <td bgcolor="#ffafaf"></td>
 134                                 <td></td>
 135                                 <td></td>
 136                                 <td></td>
 137                         </tr>
 138                         <tr>
 139                                 <td>Taylor</td>
 140                                 <td bgcolor="#ccff00"></td>
 141                                 <td bgcolor="#0000ff"></td>
 142                                 <td bgcolor="#cc00ff"></td>
 143                                 <td bgcolor="#ff0000"></td>
 144                                 <td bgcolor="#ffff00"></td>
 145                                 <td bgcolor="#ff00cc"></td>
 146                                 <td bgcolor="#ff0066"></td>
 147                                 <td bgcolor="#ff9900"></td>
 148                                 <td bgcolor="#0066ff"></td>
 149                                 <td bgcolor="#66ff00"></td>
 150                                 <td bgcolor="#33ff00"></td>
 151                                 <td bgcolor="#6600ff"></td>
 152                                 <td bgcolor="#00ff00"></td>
 153                                 <td bgcolor="#00ff66"></td>
 154                                 <td bgcolor="#ffcc00"></td>
 155                                 <td bgcolor="#ff3300"></td>
 156                                 <td bgcolor="#ff6600"></td>
 157                                 <td bgcolor="#00ccff"></td>
 158                                 <td bgcolor="#00ffcc"></td>
 159                                 <td bgcolor="#99ff00"></td>
 160                                 <td></td>
 161                                 <td></td>
 162                                 <td></td>
 163                         </tr>
 164                         <tr>
 165                                 <td>Hydrophobicity</td>
 166                                 <td bgcolor="#ad0052"></td>
 167                                 <td bgcolor="#0000ff"></td>
 168                                 <td bgcolor="#0c00f3"></td>
 169                                 <td bgcolor="#0c00f3"></td>
 170                                 <td bgcolor="#c2003d"></td>
 171                                 <td bgcolor="#0c00f3"></td>
 172                                 <td bgcolor="#0c00f3"></td>
 173                                 <td bgcolor="#6a0095"></td>
 174                                 <td bgcolor="#1500ea"></td>
 175                                 <td bgcolor="#ff0000"></td>
 176                                 <td bgcolor="#ea0015"></td>
 177                                 <td bgcolor="#0000ff"></td>
 178                                 <td bgcolor="#b0004f"></td>
 179                                 <td bgcolor="#cb0034"></td>
 180                                 <td bgcolor="#4600b9"></td>
 181                                 <td bgcolor="#5e00a1"></td>
 182                                 <td bgcolor="#61009e"></td>
 183                                 <td bgcolor="#5b00a4"></td>
 184                                 <td bgcolor="#4f00b0"></td>
 185                                 <td bgcolor="#f60009"></td>
 186                                 <td bgcolor="#0c00f3"></td>
 187                                 <td bgcolor="#680097"></td>
 188                                 <td bgcolor="#0c00f3"></td>
 189                         </tr>
 190                         <tr>
 191                                 <td>Helix Propensity</td>
 192                                 <td bgcolor="#e718e7"></td>
 193                                 <td bgcolor="#6f906f"></td>
 194                                 <td bgcolor="#1be41b"></td>
 195                                 <td bgcolor="#778877"></td>
 196                                 <td bgcolor="#23dc23"></td>
 197                                 <td bgcolor="#926d92"></td>
 198                                 <td bgcolor="#ff00ff"></td>
 199                                 <td bgcolor="#00ff00"></td>
 200                                 <td bgcolor="#758a75"></td>
 201                                 <td bgcolor="#8a758a"></td>
 202                                 <td bgcolor="#ae51ae"></td>
 203                                 <td bgcolor="#a05fa0"></td>
 204                                 <td bgcolor="#ef10ef"></td>
 205                                 <td bgcolor="#986798"></td>
 206                                 <td bgcolor="#00ff00"></td>
 207                                 <td bgcolor="#36c936"></td>
 208                                 <td bgcolor="#47b847"></td>
 209                                 <td bgcolor="#8a758a"></td>
 210                                 <td bgcolor="#21de21"></td>
 211                                 <td bgcolor="#857a85"></td>
 212                                 <td bgcolor="#49b649"></td>
 213                                 <td bgcolor="#758a75"></td>
 214                                 <td bgcolor="#c936c9"></td>
 215                         </tr>
 216                         <tr>
 217                                 <td nowrap>Strand Propensity</td>
 218                                 <td bgcolor="#5858a7"></td>
 219                                 <td bgcolor="#6b6b94"></td>
 220                                 <td bgcolor="#64649b"></td>
 221                                 <td bgcolor="#2121de"></td>
 222                                 <td bgcolor="#9d9d62"></td>
 223                                 <td bgcolor="#8c8c73"></td>
 224                                 <td bgcolor="#0000ff"></td>
 225                                 <td bgcolor="#4949b6"></td>
 226                                 <td bgcolor="#60609f"></td>
 227                                 <td bgcolor="#ecec13"></td>
 228                                 <td bgcolor="#b2b24d"></td>
 229                                 <td bgcolor="#4747b8"></td>
 230                                 <td bgcolor="#82827d"></td>
 231                                 <td bgcolor="#c2c23d"></td>
 232                                 <td bgcolor="#2323dc"></td>
 233                                 <td bgcolor="#4949b6"></td>
 234                                 <td bgcolor="#9d9d62"></td>
 235                                 <td bgcolor="#c0c03f"></td>
 236                                 <td bgcolor="#d3d32c"></td>
 237                                 <td bgcolor="#ffff00"></td>
 238                                 <td bgcolor="#4343bc"></td>
 239                                 <td bgcolor="#797986"></td>
 240                                 <td bgcolor="#4747b8"></td>
 241                         </tr>
 242                         <tr>
 243                                 <td>Turn Propensity</td>
 244                                 <td bgcolor="#2cd3d3"></td>
 245                                 <td bgcolor="#708f8f"></td>
 246                                 <td bgcolor="#ff0000"></td>
 247                                 <td bgcolor="#e81717"></td>
 248                                 <td bgcolor="#a85757"></td>
 249                                 <td bgcolor="#3fc0c0"></td>
 250                                 <td bgcolor="#778888"></td>
 251                                 <td bgcolor="#ff0000"></td>
 252                                 <td bgcolor="#708f8f"></td>
 253                                 <td bgcolor="#00ffff"></td>
 254                                 <td bgcolor="#1ce3e3"></td>
 255                                 <td bgcolor="#7e8181"></td>
 256                                 <td bgcolor="#1ee1e1"></td>
 257                                 <td bgcolor="#1ee1e1"></td>
 258                                 <td bgcolor="#f60909"></td>
 259                                 <td bgcolor="#e11e1e"></td>
 260                                 <td bgcolor="#738c8c"></td>
 261                                 <td bgcolor="#738c8c"></td>
 262                                 <td bgcolor="#9d6262"></td>
 263                                 <td bgcolor="#07f8f8"></td>
 264                                 <td bgcolor="#f30c0c"></td>
 265                                 <td bgcolor="#7c8383"></td>
 266                                 <td bgcolor="#5ba4a4"></td>
 267                         </tr>
 268                         <tr>
 269                                 <td>Buried Index</td>
 270                                 <td bgcolor="#00a35c"></td>
 271                                 <td bgcolor="#00fc03"></td>
 272                                 <td bgcolor="#00eb14"></td>
 273                                 <td bgcolor="#00eb14"></td>
 274                                 <td bgcolor="#0000ff"></td>
 275                                 <td bgcolor="#00f10e"></td>
 276                                 <td bgcolor="#00f10e"></td>
 277                                 <td bgcolor="#009d62"></td>
 278                                 <td bgcolor="#00d52a"></td>
 279                                 <td bgcolor="#0054ab"></td>
 280                                 <td bgcolor="#007b84"></td>
 281                                 <td bgcolor="#00ff00"></td>
 282                                 <td bgcolor="#009768"></td>
 283                                 <td bgcolor="#008778"></td>
 284                                 <td bgcolor="#00e01f"></td>
 285                                 <td bgcolor="#00d52a"></td>
 286                                 <td bgcolor="#00db24"></td>
 287                                 <td bgcolor="#00a857"></td>
 288                                 <td bgcolor="#00e619"></td>
 289                                 <td bgcolor="#005fa0"></td>
 290                                 <td bgcolor="#00eb14"></td>
 291                                 <td bgcolor="#00b649"></td>
 292                                 <td bgcolor="#00f10e"></td>
 293                         </tr>
 294                 </table>
 295                 </td>
 296         </tr>
 297 </table>
 298 <p>&nbsp;</p>
 299 <p><strong>Nucleotide Colour Schemes</strong></p>
 300 <table border="1">
 301         <tr>
 302                 <td>
 303                 <table border="1">
 304                         <tr>
 305                                 <td nowrap></td>
 306                                 <td>A</td> <!--Adenine-->
 307                             <td>C</td> <!--Cytosine-->
 308                         <td>G</td> <!--Guanine-->
 309                         <td>T</td> <!--Thymine-->
 310                         <td>U</td> <!--Uracil-->
 311                         <td>I</td> <!--Inosine-->
 312                         <td>X</td> <!--Xanthine-->
 313                         <td>R</td> <!--Unknown Purine-->
 314                         <td>Y</td> <!--Unknown Pyrimidine-->
 315                         <td>N</td> <!--Unknown-->
 316                         <td>W</td> <!--Weak nucleotide (A or T)-->
 317                         <td>S</td> <!--Strong nucleotide (G or C)-->
 318                         <td>M</td> <!--Amino (A or C)-->
 319                         <td>K</td> <!--Keto (G or T)-->
 320                         <td>B</td> <!--Not A (G or C or T)-->
 321                         <td>H</td> <!--Not G (A or C or T)-->
 322                         <td>D</td> <!--Not C (A or G or T)-->
 323                         <td>V</td> <!--Not T (A or G or C-->
 324                         </tr>
 325                         <tr>
 326                                 <td height="24">Nucleotide</td>
 327                                 <td bgcolor="#64F73F"></td>
 328                                 <td bgcolor="#FFB340"></td>
 329                         <td bgcolor="#EB413C"></td>
 330                         <td bgcolor="#3C88EE"></td>
 331                         <td bgcolor="#3C88EE"></td>
 332                         <td></td>
 333                         <td></td>
 334                         <td></td>
 335                         <td></td>
 336                         <td></td>
 337                         <td></td>
 338                         <td></td>
 339                         <td></td>
 340                         <td></td>
 341                         <td></td>
 342                         <td></td>
 343                         <td></td>
 344                         <td></td>
 345                         </tr>
 346                         <tr>
 347                                 <td height="24">Purine/Pyrimidine</td>
 348                                 <td bgcolor="#FF83FA"></td>
 349                                 <td bgcolor="#40E0D0"></td>
 350                         <td bgcolor="#FF83FA"></td>
 351                         <td bgcolor="#40E0D0"></td>
 352                         <td bgcolor="#40E0D0"></td>
 353                         <td></td>
 354                         <td></td>
 355                         <td bgcolor="#FF83FA"></td>
 356                         <td bgcolor="#40E0D0"></td>
 357                         <td></td>
 358                         <td></td>
 359                         <td></td>
 360                         <td></td>
 361                         <td></td>
 362                         <td></td>
 363                         <td></td>
 364                         <td></td>
 365                         <td></td>
 366                         </tr>
 367                 </table>
 368                 </td>
 369         </tr>
 370 </table>
 371
 372
 373 </div>
 374 <p align="center">&nbsp;</p>
 375 </body>
 376 </html>