1 from Bio import Alphabet
2 """
3 Reduced (redundant or simplified) alphabets are used to represent protein sequences using an
4 alternative alphabet which lumps together several amino-acids into one letter, based
5 on physico-chemical traits. For example, all the aliphatics (I,L,V) are usually
6 quite interchangeable, so many sequence studies group them into one letter
7
8 Examples of reduced alphabets are available in:
9
10 http://viscose.ifg.uni-muenster.de/html/alphabets.html
11
12 Bio.utils.reduce_sequence is used to take a Protein alphabet, and reduce it using one of
13 the tables here, or a user-defined table.
14 """
15
16
17
18
19 murphy_15_tab = {"L": "L",
20 "V": "L",
21 "I": "L",
22 "M": "L",
23 "C": "C",
24 "A": "A",
25 "G": "G",
26 "S": "S",
27 "T": "T",
28 "P": "P",
29 "F": "F",
30 "Y": "F",
31 "W": "W",
32 "E": "E",
33 "D": "D",
34 "N": "N",
35 "Q": "Q",
36 "K": "K",
37 "R": "K",
38 "H": "H"}
39
40 -class Murphy15(Alphabet.ProteinAlphabet):
43 murphy_15 = Murphy15()
44
45 murphy_10_tab = {"L": "L",
46 "V": "L",
47 "I": "L",
48 "M": "L",
49 "C": "C",
50 "A": "A",
51 "G": "G",
52 "S": "S",
53 "T": "S",
54 "P": "P",
55 "F": "F",
56 "Y": "F",
57 "W": "F",
58 "E": "E",
59 "D": "E",
60 "N": "E",
61 "Q": "E",
62 "K": "K",
63 "R": "K",
64 "H": "H"}
65 -class Murphy10(Alphabet.ProteinAlphabet):
68 murphy_10 = Murphy10()
69
70 murphy_8_tab = {"L": "L",
71 "V": "L",
72 "I": "L",
73 "M": "L",
74 "C": "L",
75 "A": "A",
76 "G": "A",
77 "S": "S",
78 "T": "S",
79 "P": "P",
80 "F": "F",
81 "Y": "F",
82 "W": "F",
83 "E": "E",
84 "D": "E",
85 "N": "E",
86 "Q": "E",
87 "K": "K",
88 "R": "K",
89 "H": "H"}
90
91 -class Murphy8(Alphabet.ProteinAlphabet):
94 murphy_8 = Murphy8()
95
96 murphy_4_tab = {"L": "L",
97 "V": "L",
98 "I": "L",
99 "M": "L",
100 "C": "L",
101 "A": "A",
102 "G": "A",
103 "S": "A",
104 "T": "A",
105 "P": "A",
106 "F": "F",
107 "Y": "F",
108 "W": "F",
109 "E": "E",
110 "D": "E",
111 "N": "E",
112 "Q": "E",
113 "K": "E",
114 "R": "E",
115 "H": "E"}
116
117 -class Murphy4(Alphabet.ProteinAlphabet):
120 murphy_4 = Murphy4()
121
122 hp_model_tab = {"A": "P",
123 "G": "P",
124 "T": "P",
125 "S": "P",
126 "N": "P",
127 "Q": "P",
128 "D": "P",
129 "E": "P",
130 "H": "P",
131 "R": "P",
132 "K": "P",
133 "P": "P",
134 "C": "H",
135 "M": "H",
136 "F": "H",
137 "I": "H",
138 "L": "H",
139 "V": "H",
140 "W": "H",
141 "Y": "H"}
142
143 -class HPModel(Alphabet.ProteinAlphabet):
146 hp_model = HPModel()
147
148 pc_5_table = {"I": "A",
149 "V": "A",
150 "L": "A",
151 "F": "R",
152 "Y": "R",
153 "W": "R",
154 "H": "R",
155 "K": "C",
156 "R": "C",
157 "D": "C",
158 "E": "C",
159 "G": "T",
160 "A": "T",
161 "C": "T",
162 "S": "T",
163 "T": "D",
164 "M": "D",
165 "Q": "D",
166 "N": "D",
167 "P": "D"}
168
169 -class PC5(Alphabet.ProteinAlphabet):
172 hp_model = HPModel()
173