JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protein products
[jalview.git] / help / html / colourSchemes / index.html
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22 <head>
23 <title>Colour Schemes</title>
24 <style type="text/css">
25 <!--
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32 </style>
33 </head>
34 <body>
35   <p>
36     <strong>Colour schemes</strong>
37   </p>
38   <p>Jalview allows the user to set a background colour for the
39     whole alignment view or for each group defined on regions within it.</p>
40   <p>To change the background colour, simply select the colour from
41     the &quot;Colour&quot; menu.</p>
42   <p>To change the colour of a group, right click on any residue
43     within a group and use the popup menu to define the group colour.</p>
44   <p>At the top of the &quot;Colour&quot; menu the tick box
45     &quot;Apply Background Colour to all groups&quot;. This is ticked by
46     default so that a chosen colour scheme will be applied to all
47     existing groups. If you wish to maintain the colour scheme for
48     defined groups, make sure you deselect this option before changing
49     the background colour.</p>
50   <p>
51     The <strong>&quot;Colour&#8594;<a
52       href="../colourSchemes/textcolour.html"
53     >Colour Text...</a>&quot;
54     </strong> entry opens a dialog box to set a different text colour for light
55     and dark background, and the intensity threshold for transition
56     between them.
57   </p>
58   <p>The default colour schemes are summarised in the table below:
59   <div align="center">
60     <p>&nbsp;</p>
61     <p>
62       <strong>Protein Colour Schemes</strong>
63     </p>
64     <table border="1">
65       <tr>
66         <td>
67           <table border="1">
68             <tr>
69               <td nowrap></td>
70               <td>A</td>
71               <td>R</td>
72               <td>N</td>
73               <td>D</td>
74               <td>C</td>
75               <td>Q</td>
76               <td>E</td>
77               <td>G</td>
78               <td>H</td>
79               <td>I</td>
80               <td>L</td>
81               <td>K</td>
82               <td>M</td>
83               <td>F</td>
84               <td>P</td>
85               <td>S</td>
86               <td>T</td>
87               <td>W</td>
88               <td>Y</td>
89               <td>V</td>
90               <td>B</td>
91               <td>X</td>
92               <td>Z</td>
93             </tr>
94             <tr>
95               <td height="24">Clustal</td>
96               <td bgcolor="#80a0f0"></td>
97               <td bgcolor="#f01505"></td>
98               <td bgcolor="#00ff00"></td>
99               <td bgcolor="#c048c0"></td>
100               <td bgcolor="#f08080"></td>
101               <td bgcolor="#00ff00"></td>
102               <td bgcolor="#c048c0"></td>
103               <td bgcolor="#f09048"></td>
104               <td bgcolor="#15a4a4"></td>
105               <td bgcolor="#80a0f0"></td>
106               <td bgcolor="#80a0f0"></td>
107               <td bgcolor="#f01505"></td>
108               <td bgcolor="#80a0f0"></td>
109               <td bgcolor="#80a0f0"></td>
110               <td bgcolor="#ffff00"></td>
111               <td bgcolor="#00ff00"></td>
112               <td bgcolor="#00ff00"></td>
113               <td bgcolor="#80a0f0"></td>
114               <td bgcolor="#15a4a4"></td>
115               <td bgcolor="#80a0f0"></td>
116               <td></td>
117               <td></td>
118               <td></td>
119             </tr>
120             <tr>
121               <td height="24">Zappo</td>
122               <td bgcolor="#ffafaf"></td>
123               <td bgcolor="#6464ff"></td>
124               <td bgcolor="#00ff00"></td>
125               <td bgcolor="#ff0000"></td>
126               <td bgcolor="#ffff00"></td>
127               <td bgcolor="#00ff00"></td>
128               <td bgcolor="#ff0000"></td>
129               <td bgcolor="#ff00ff"></td>
130               <td bgcolor="#6464ff"></td>
131               <td bgcolor="#ffafaf"></td>
132               <td bgcolor="#ffafaf"></td>
133               <td bgcolor="#6464ff"></td>
134               <td bgcolor="#ffafaf"></td>
135               <td bgcolor="#ffc800"></td>
136               <td bgcolor="#ff00ff"></td>
137               <td bgcolor="#00ff00"></td>
138               <td bgcolor="#00ff00"></td>
139               <td bgcolor="#ffc800"></td>
140               <td bgcolor="#ffc800"></td>
141               <td bgcolor="#ffafaf"></td>
142               <td></td>
143               <td></td>
144               <td></td>
145             </tr>
146             <tr>
147               <td>Taylor</td>
148               <td bgcolor="#ccff00"></td>
149               <td bgcolor="#0000ff"></td>
150               <td bgcolor="#cc00ff"></td>
151               <td bgcolor="#ff0000"></td>
152               <td bgcolor="#ffff00"></td>
153               <td bgcolor="#ff00cc"></td>
154               <td bgcolor="#ff0066"></td>
155               <td bgcolor="#ff9900"></td>
156               <td bgcolor="#0066ff"></td>
157               <td bgcolor="#66ff00"></td>
158               <td bgcolor="#33ff00"></td>
159               <td bgcolor="#6600ff"></td>
160               <td bgcolor="#00ff00"></td>
161               <td bgcolor="#00ff66"></td>
162               <td bgcolor="#ffcc00"></td>
163               <td bgcolor="#ff3300"></td>
164               <td bgcolor="#ff6600"></td>
165               <td bgcolor="#00ccff"></td>
166               <td bgcolor="#00ffcc"></td>
167               <td bgcolor="#99ff00"></td>
168               <td></td>
169               <td></td>
170               <td></td>
171             </tr>
172             <tr>
173               <td>Hydrophobicity</td>
174               <td bgcolor="#ad0052"></td>
175               <td bgcolor="#0000ff"></td>
176               <td bgcolor="#0c00f3"></td>
177               <td bgcolor="#0c00f3"></td>
178               <td bgcolor="#c2003d"></td>
179               <td bgcolor="#0c00f3"></td>
180               <td bgcolor="#0c00f3"></td>
181               <td bgcolor="#6a0095"></td>
182               <td bgcolor="#1500ea"></td>
183               <td bgcolor="#ff0000"></td>
184               <td bgcolor="#ea0015"></td>
185               <td bgcolor="#0000ff"></td>
186               <td bgcolor="#b0004f"></td>
187               <td bgcolor="#cb0034"></td>
188               <td bgcolor="#4600b9"></td>
189               <td bgcolor="#5e00a1"></td>
190               <td bgcolor="#61009e"></td>
191               <td bgcolor="#5b00a4"></td>
192               <td bgcolor="#4f00b0"></td>
193               <td bgcolor="#f60009"></td>
194               <td bgcolor="#0c00f3"></td>
195               <td bgcolor="#680097"></td>
196               <td bgcolor="#0c00f3"></td>
197             </tr>
198             <tr>
199               <td>Helix Propensity</td>
200               <td bgcolor="#e718e7"></td>
201               <td bgcolor="#6f906f"></td>
202               <td bgcolor="#1be41b"></td>
203               <td bgcolor="#778877"></td>
204               <td bgcolor="#23dc23"></td>
205               <td bgcolor="#926d92"></td>
206               <td bgcolor="#ff00ff"></td>
207               <td bgcolor="#00ff00"></td>
208               <td bgcolor="#758a75"></td>
209               <td bgcolor="#8a758a"></td>
210               <td bgcolor="#ae51ae"></td>
211               <td bgcolor="#a05fa0"></td>
212               <td bgcolor="#ef10ef"></td>
213               <td bgcolor="#986798"></td>
214               <td bgcolor="#00ff00"></td>
215               <td bgcolor="#36c936"></td>
216               <td bgcolor="#47b847"></td>
217               <td bgcolor="#8a758a"></td>
218               <td bgcolor="#21de21"></td>
219               <td bgcolor="#857a85"></td>
220               <td bgcolor="#49b649"></td>
221               <td bgcolor="#758a75"></td>
222               <td bgcolor="#c936c9"></td>
223             </tr>
224             <tr>
225               <td nowrap>Strand Propensity</td>
226               <td bgcolor="#5858a7"></td>
227               <td bgcolor="#6b6b94"></td>
228               <td bgcolor="#64649b"></td>
229               <td bgcolor="#2121de"></td>
230               <td bgcolor="#9d9d62"></td>
231               <td bgcolor="#8c8c73"></td>
232               <td bgcolor="#0000ff"></td>
233               <td bgcolor="#4949b6"></td>
234               <td bgcolor="#60609f"></td>
235               <td bgcolor="#ecec13"></td>
236               <td bgcolor="#b2b24d"></td>
237               <td bgcolor="#4747b8"></td>
238               <td bgcolor="#82827d"></td>
239               <td bgcolor="#c2c23d"></td>
240               <td bgcolor="#2323dc"></td>
241               <td bgcolor="#4949b6"></td>
242               <td bgcolor="#9d9d62"></td>
243               <td bgcolor="#c0c03f"></td>
244               <td bgcolor="#d3d32c"></td>
245               <td bgcolor="#ffff00"></td>
246               <td bgcolor="#4343bc"></td>
247               <td bgcolor="#797986"></td>
248               <td bgcolor="#4747b8"></td>
249             </tr>
250             <tr>
251               <td>Turn Propensity</td>
252               <td bgcolor="#2cd3d3"></td>
253               <td bgcolor="#708f8f"></td>
254               <td bgcolor="#ff0000"></td>
255               <td bgcolor="#e81717"></td>
256               <td bgcolor="#a85757"></td>
257               <td bgcolor="#3fc0c0"></td>
258               <td bgcolor="#778888"></td>
259               <td bgcolor="#ff0000"></td>
260               <td bgcolor="#708f8f"></td>
261               <td bgcolor="#00ffff"></td>
262               <td bgcolor="#1ce3e3"></td>
263               <td bgcolor="#7e8181"></td>
264               <td bgcolor="#1ee1e1"></td>
265               <td bgcolor="#1ee1e1"></td>
266               <td bgcolor="#f60909"></td>
267               <td bgcolor="#e11e1e"></td>
268               <td bgcolor="#738c8c"></td>
269               <td bgcolor="#738c8c"></td>
270               <td bgcolor="#9d6262"></td>
271               <td bgcolor="#07f8f8"></td>
272               <td bgcolor="#f30c0c"></td>
273               <td bgcolor="#7c8383"></td>
274               <td bgcolor="#5ba4a4"></td>
275             </tr>
276             <tr>
277               <td>Buried Index</td>
278               <td bgcolor="#00a35c"></td>
279               <td bgcolor="#00fc03"></td>
280               <td bgcolor="#00eb14"></td>
281               <td bgcolor="#00eb14"></td>
282               <td bgcolor="#0000ff"></td>
283               <td bgcolor="#00f10e"></td>
284               <td bgcolor="#00f10e"></td>
285               <td bgcolor="#009d62"></td>
286               <td bgcolor="#00d52a"></td>
287               <td bgcolor="#0054ab"></td>
288               <td bgcolor="#007b84"></td>
289               <td bgcolor="#00ff00"></td>
290               <td bgcolor="#009768"></td>
291               <td bgcolor="#008778"></td>
292               <td bgcolor="#00e01f"></td>
293               <td bgcolor="#00d52a"></td>
294               <td bgcolor="#00db24"></td>
295               <td bgcolor="#00a857"></td>
296               <td bgcolor="#00e619"></td>
297               <td bgcolor="#005fa0"></td>
298               <td bgcolor="#00eb14"></td>
299               <td bgcolor="#00b649"></td>
300               <td bgcolor="#00f10e"></td>
301             </tr>
302           </table>
303         </td>
304       </tr>
305     </table>
306     <p>&nbsp;</p>
307     <p>
308       <strong>Nucleotide Colour Schemes</strong>
309     </p>
310     <table border="1">
311       <tr>
312         <td>
313           <table border="1">
314             <tr>
315               <td nowrap></td>
316               <td>A</td>
317               <!--Adenine-->
318               <td>C</td>
319               <!--Cytosine-->
320               <td>G</td>
321               <!--Guanine-->
322               <td>T</td>
323               <!--Thymine-->
324               <td>U</td>
325               <!--Uracil-->
326               <td>I</td>
327               <!--Inosine-->
328               <td>X</td>
329               <!--Xanthine-->
330               <td>R</td>
331               <!--Unknown Purine-->
332               <td>Y</td>
333               <!--Unknown Pyrimidine-->
334               <td>N</td>
335               <!--Unknown-->
336               <td>W</td>
337               <!--Weak nucleotide (A or T)-->
338               <td>S</td>
339               <!--Strong nucleotide (G or C)-->
340               <td>M</td>
341               <!--Amino (A or C)-->
342               <td>K</td>
343               <!--Keto (G or T)-->
344               <td>B</td>
345               <!--Not A (G or C or T)-->
346               <td>H</td>
347               <!--Not G (A or C or T)-->
348               <td>D</td>
349               <!--Not C (A or G or T)-->
350               <td>V</td>
351               <!--Not T (A or G or C-->
352             </tr>
353             <tr>
354               <td height="24">Nucleotide</td>
355               <td bgcolor="#64F73F"></td>
356               <td bgcolor="#FFB340"></td>
357               <td bgcolor="#EB413C"></td>
358               <td bgcolor="#3C88EE"></td>
359               <td bgcolor="#3C88EE"></td>
360               <td></td>
361               <td></td>
362               <td></td>
363               <td></td>
364               <td></td>
365               <td></td>
366               <td></td>
367               <td></td>
368               <td></td>
369               <td></td>
370               <td></td>
371               <td></td>
372               <td></td>
373             </tr>
374             <tr>
375               <td height="24">Purine/Pyrimidine</td>
376               <td bgcolor="#FF83FA"></td>
377               <td bgcolor="#40E0D0"></td>
378               <td bgcolor="#FF83FA"></td>
379               <td bgcolor="#40E0D0"></td>
380               <td bgcolor="#40E0D0"></td>
381               <td></td>
382               <td></td>
383               <td bgcolor="#FF83FA"></td>
384               <td bgcolor="#40E0D0"></td>
385               <td></td>
386               <td></td>
387               <td></td>
388               <td></td>
389               <td></td>
390               <td></td>
391               <td></td>
392               <td></td>
393               <td></td>
394             </tr>
395           </table>
396         </td>
397       </tr>
398     </table>
399
400
401   </div>
402   <p align="center">&nbsp;</p>
403 </body>
404 </html>