3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
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.
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.
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.
23 <title>Nucleotide Colour Scheme</title>
24 <style type="text/css">
35 <strong>Nucleotide Ambiguity Colours</strong>
40 This colour scheme was devised by Suzanne Duce and the Jalview Team to highlight ambiguity codes used in nucleotide sequences.
43 The use of X to represent an unknown base is acknowledged, but this is not recommended as the symbol refers to xanthine (see IUPAC-IUB Commission on Biochemical Nomenclature (CBN). <a href="https://iupac.qmul.ac.uk/misc/naabb.html">Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents.</a>)
46 <table width="200" border="1">
48 <td bgcolor="#f0fff0">A</td>
52 <td bgcolor="#f0fff0">C</td>
56 <td bgcolor="#f0fff0">G</td>
60 <td bgcolor="#f0fff0">T</td>
64 <td bgcolor="#f0fff0">U</td>
68 <td bgcolor="#ffffff">I</td>
72 <td bgcolor="#4f6f6f">X</td>
73 <td>Unknown (sometimes Xanthine)</td>
76 <td bgcolor="#CD5C5C">R</td>
77 <td>Unknown Purine</td>
80 <td bgcolor="#008000">Y</td>
81 <td>Unknown Pyrimidine</td>
84 <td bgcolor="#4682B4">W</td>
85 <td>Weak nucleotide (A or T)</td>
88 <td bgcolor="#FF8C00">S</td>
89 <td>Strong nucleotide (G or C)</td>
92 <td bgcolor="#9ACD32">M</td>
93 <td>Amino (A or C)</td>
96 <td bgcolor="#9932CC">K</td>
97 <td>Keto (G or T)</td>
100 <td bgcolor="#8b4513">B</td>
101 <td>Not A (G or C or T)</td>
104 <td bgcolor="#808080">H</td>
105 <td>Not G (A or C or T)</td>
108 <td bgcolor="#483D8B">D</td>
109 <td>Not C (A or G or T)</td>
112 <td bgcolor="#b8860b">V</td>
113 <td>Not T (A or G or C)</td>
116 <td bgcolor="#2f4f4f">N</td>