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-- J.Ostell 10/18/91
--
Seq-code-set ::= {
codes { -- codes
{ -- IUPACna
code iupacna ,
num 25 , -- continuous 65-89
one-letter TRUE , -- all one letter codes
start-at 65 , -- starts with A, ASCII 65
table {
{ symbol "A", name "Adenine" },
{ symbol "B" , name "G or T or C" },
{ symbol "C", name "Cytosine" },
{ symbol "D", name "G or A or T" },
{ symbol "", name "" },
{ symbol "", name "" },
{ symbol "G", name "Guanine" },
{ symbol "H", name "A or C or T" } ,
{ symbol "", name "" },
{ symbol "", name "" },
{ symbol "K", name "G or T" },
{ symbol "", name ""},
{ symbol "M", name "A or C" },
{ symbol "N", name "A or G or C or T" } ,
{ symbol "", name "" },
{ symbol "", name "" },
{ symbol "", name ""},
{ symbol "R", name "G or A"},
{ symbol "S", name "G or C"},
{ symbol "T", name "Thymine"},
{ symbol "", name ""},
{ symbol "V", name "G or C or A"},
{ symbol "W", name "A or T" },
{ symbol "", name ""},
{ symbol "Y", name "T or C"}
} , -- end of table
comps { -- complements
84,
86,
71,
72,
69,
70,
67,
68,
73,
74,
77,
76,
75,
78,
79,
80,
81,
89,
83,
65,
85,
66,
87,
88,
82
}
} ,
{ -- IUPACaa
code iupacaa ,
num 26 , -- continuous 65-90
one-letter TRUE , -- all one letter codes
start-at 65 , -- starts with A, ASCII 65
table {
{ symbol "A", name "Alanine" },
{ symbol "B" , name "Asp or Asn" },
{ symbol "C", name "Cysteine" },
{ symbol "D", name "Aspartic Acid" },
{ symbol "E", name "Glutamic Acid" },
{ symbol "F", name "Phenylalanine" },
{ symbol "G", name "Glycine" },
{ symbol "H", name "Histidine" } ,
{ symbol "I", name "Isoleucine" },
{ symbol "J", name "Leu or Ile" },
{ symbol "K", name "Lysine" },
{ symbol "L", name "Leucine" },
{ symbol "M", name "Methionine" },
{ symbol "N", name "Asparagine" } ,
{ symbol "O", name "Pyrrolysine" },
{ symbol "P", name "Proline" },
{ symbol "Q", name "Glutamine"},
{ symbol "R", name "Arginine"},
{ symbol "S", name "Serine"},
{ symbol "T", name "Threonine"},
{ symbol "U", name "Selenocysteine"}, -- was empty
{ symbol "V", name "Valine"},
{ symbol "W", name "Tryptophan" },
{ symbol "X", name "Undetermined or atypical"},
{ symbol "Y", name "Tyrosine"},
{ symbol "Z", name "Glu or Gln" }
} -- end of table
} ,
{ -- IUPACeaa
code ncbieaa ,
num 49 , -- continuous 42-90
one-letter TRUE , -- all one letter codes
start-at 42 , -- starts with *, ASCII 42
table {
{ symbol "*", name "Termination" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "-", name "Gap" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "", name "" } ,
{ symbol "A", name "Alanine" },
{ symbol "B" , name "Asp or Asn" },
{ symbol "C", name "Cysteine" },
{ symbol "D", name "Aspartic Acid" },
{ symbol "E", name "Glutamic Acid" },
{ symbol "F", name "Phenylalanine" },
{ symbol "G", name "Glycine" },
{ symbol "H", name "Histidine" } ,
{ symbol "I", name "Isoleucine" },
{ symbol "J", name "Leu or Ile" },
{ symbol "K", name "Lysine" },
{ symbol "L", name "Leucine" },
{ symbol "M", name "Methionine" },
{ symbol "N", name "Asparagine" } ,
{ symbol "O", name "Pyrrolysine" },
{ symbol "P", name "Proline" },
{ symbol "Q", name "Glutamine"},
{ symbol "R", name "Arginine"},
{ symbol "S", name "Serine"},
{ symbol "T", name "Threonine"},
{ symbol "U", name "Selenocysteine"},
{ symbol "V", name "Valine"},
{ symbol "W", name "Tryptophan" },
{ symbol "X", name "Undetermined or atypical"},
{ symbol "Y", name "Tyrosine"},
{ symbol "Z", name "Glu or Gln" }
} -- end of table
} ,
{ -- IUPACaa3
code iupacaa3 ,
num 28 , -- continuous 0-27
one-letter FALSE , -- all 3 letter codes
table {
{ symbol "---", name "Gap" } ,
{ symbol "Ala", name "Alanine" },
{ symbol "Asx" , name "Asp or Asn" },
{ symbol "Cys", name "Cysteine" },
{ symbol "Asp", name "Aspartic Acid" },
{ symbol "Glu", name "Glutamic Acid" },
{ symbol "Phe", name "Phenylalanine" },
{ symbol "Gly", name "Glycine" },
{ symbol "His", name "Histidine" } ,
{ symbol "Ile", name "Isoleucine" },
{ symbol "Lys", name "Lysine" },
{ symbol "Leu", name "Leucine" },
{ symbol "Met", name "Methionine" },
{ symbol "Asn", name "Asparagine" } ,
{ symbol "Pro", name "Proline" },
{ symbol "Gln", name "Glutamine"},
{ symbol "Arg", name "Arginine"},
{ symbol "Ser", name "Serine"},
{ symbol "Thr", name "Threonine"},
{ symbol "Val", name "Valine"},
{ symbol "Trp", name "Tryptophan" },
{ symbol "Xxx", name "Undetermined or atypical"},
{ symbol "Tyr", name "Tyrosine"},
{ symbol "Glx", name "Glu or Gln" },
{ symbol "Sec", name "Selenocysteine"},
{ symbol "Ter", name "Termination" },
{ symbol "Pyl", name "Pyrrolysine"},
{ symbol "Xle", name "Leu or Ile"}
} -- end of table
} ,
{ -- NCBIstdaa
code ncbistdaa ,
num 28 , -- continuous 0-27
one-letter TRUE , -- all one letter codes
table {
{ symbol "-", name "Gap" } , -- 0
{ symbol "A", name "Alanine" }, -- 1
{ symbol "B" , name "Asp or Asn" }, -- 2
{ symbol "C", name "Cysteine" }, -- 3
{ symbol "D", name "Aspartic Acid" }, -- 4
{ symbol "E", name "Glutamic Acid" }, -- 5
{ symbol "F", name "Phenylalanine" }, -- 6
{ symbol "G", name "Glycine" }, -- 7
{ symbol "H", name "Histidine" } , -- 8
{ symbol "I", name "Isoleucine" }, -- 9
{ symbol "K", name "Lysine" }, -- 10
{ symbol "L", name "Leucine" }, -- 11
{ symbol "M", name "Methionine" }, -- 12
{ symbol "N", name "Asparagine" } , -- 13
{ symbol "P", name "Proline" }, -- 14
{ symbol "Q", name "Glutamine"}, -- 15
{ symbol "R", name "Arginine"}, -- 16
{ symbol "S", name "Serine"}, -- 17
{ symbol "T", name "Threoine"}, -- 18
{ symbol "V", name "Valine"}, -- 19
{ symbol "W", name "Tryptophan" }, -- 20
{ symbol "X", name "Undetermined or atypical"}, -- 21
{ symbol "Y", name "Tyrosine"}, -- 22
{ symbol "Z", name "Glu or Gln" }, -- 23
{ symbol "U", name "Selenocysteine"}, -- 24
{ symbol "*", name "Termination" }, -- 25
{ symbol "O", name "Pyrrolysine" }, -- 26
{ symbol "J", name "Leu or Ile" } -- 27
} -- end of table
} ,
{ -- NCBI2na
code ncbi2na ,
num 4 , -- continuous 0-3
one-letter TRUE , -- all one letter codes
table {
{ symbol "A", name "Adenine" },
{ symbol "C", name "Cytosine" },
{ symbol "G", name "Guanine" },
{ symbol "T", name "Thymine/Uracil"}
} , -- end of table
comps { -- complements
3,
2,
1,
0
}
} ,
{ -- NCBI4na
code ncbi4na ,
num 16 , -- continuous 0-15
one-letter TRUE , -- all one letter codes
table {
{ symbol "-", name "Gap" } ,
{ symbol "A", name "Adenine" },
{ symbol "C", name "Cytosine" },
{ symbol "M", name "A or C" },
{ symbol "G", name "Guanine" },
{ symbol "R", name "G or A"},
{ symbol "S", name "G or C"},
{ symbol "V", name "G or C or A"},
{ symbol "T", name "Thymine/Uracil"},
{ symbol "W", name "A or T" },
{ symbol "Y", name "T or C"} ,
{ symbol "H", name "A or C or T" } ,
{ symbol "K", name "G or T" },
{ symbol "D", name "G or A or T" },
{ symbol "B" , name "G or T or C" },
{ symbol "N", name "A or G or C or T" }
} , -- end of table
comps { -- complements
0 ,
8 ,
4 ,
12,
2 ,
10,
6 ,
14,
1 ,
9 ,
5 ,
13,
3 ,
11,
7 ,
15
}
} ,
} , -- end of codes
maps {
{
from iupacna ,
to ncbi2na ,
num 25 ,
start-at 65 ,
table {
0, -- A -> A
1, -- B -> C
1, -- C -> C
2, -- D -> G
255,
255,
2, -- G -> G
0, -- H -> A
255,
255,
2, -- K -> G
255,
1, -- M -> C
0, -- N -> A
255,
255,
255,
2, -- R -> G
1, -- S -> C
3, -- T -> T
255,
0, -- V -> A
3, -- W -> T
255,
3 } -- Y -> T
} ,
{
from iupacna ,
to ncbi4na ,
num 26 ,
start-at 64 ,
table {
0, -- @ used by FastaToSeqEntry to convert hyphen to gap
1, -- A
14, -- B
2, -- C
13, -- D
255,
255,
4, -- G
11, -- H
255,
255,
12, -- K
255,
3, -- M
15, -- N
255,
255,
255,
5, -- R
6, -- S
8, -- T
255,
7, -- V
9, -- W
255,
10 } -- Y
} ,
{
from ncbi2na ,
to iupacna ,
num 4 ,
table {
65, -- A
67, -- C
71, -- G
84 } -- T
} ,
{
from ncbi2na ,
to ncbi4na ,
num 4 ,
table {
1, -- A
2, -- C
4, -- G
8 } -- T
} ,
{
from ncbi4na ,
to iupacna ,
num 16 ,
table {
78, -- gap -> N
65, -- A
67, -- C
77, -- M
71, -- G
82, -- R
83, -- S
86, -- V
84, -- T
87, -- W
89, -- Y
72, -- H
75, -- K
68, -- D
66, -- B
78 } -- N
} ,
{
from ncbi4na ,
to ncbi2na ,
num 16 ,
table {
3, -- gap -> T
0, -- A -> A
1, -- C -> C
1, -- M -> C
2, -- G -> G
2, -- R -> G
1, -- S -> C
0, -- V -> A
3, -- T -> T
3, -- W -> T
3, -- Y -> T
0, -- H -> A
2, -- K -> G
2, -- D -> G
1, -- B -> C
0 } -- N -> A
} ,
{
from iupacaa ,
to ncbieaa ,
num 26 ,
start-at 65 ,
table {
65 , -- they map directly
66 ,
67 ,
68,
69,
70,
71,
72,
73,
74, -- J - was 255
75,
76,
77,
78,
79, -- O - was 255
80,
81,
82,
83,
84,
85, -- U - was 255
86,
87,
88,
89,
90 }
} ,
{
from ncbieaa ,
to iupacaa ,
num 49 ,
start-at 42 ,
table {
88 , -- termination -> X
255,
255,
88, -- Gap -> X
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
65 , -- from here they map directly
66 ,
67 ,
68,
69,
70,
71,
72,
73,
74, -- J - was 255
75,
76,
77,
78,
79, -- O - was 255
80,
81,
82,
83,
84,
85, -- U was -> X 88
86,
87,
88,
89,
90 }
} ,
{
from iupacaa ,
to ncbistdaa ,
num 26 ,
start-at 65 ,
table {
1 , -- they map directly
2 ,
3 ,
4,
5,
6,
7,
8,
9,
27, -- J - was 255
10,
11,
12,
13,
26, -- O - was 255
14,
15,
16,
17,
18,
24, -- U - was 255
19,
20,
21,
22,
23 }
} ,
{
from ncbieaa ,
to ncbistdaa ,
num 49 ,
start-at 42 ,
table {
25, -- termination
255,
255,
0, -- Gap
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
255,
1 , -- they map directly
2 ,
3 ,
4,
5,
6,
7,
8,
9,
27, -- J - was 255
10,
11,
12,
13,
26, -- O - was 255
14,
15,
16,
17,
18,
24, -- U
19,
20,
21,
22,
23 }
} ,
{
from ncbistdaa ,
to ncbieaa ,
num 28 ,
table {
45 , -- "-"
65 , -- they map directly with holes for O and J
66 ,
67 ,
68,
69,
70,
71,
72,
73,
75,
76,
77,
78,
80,
81,
82,
83,
84,
86,
87,
88,
89,
90,
85, -- U
42, -- *
79, -- O - new
74} -- J - new
} ,
{
from ncbistdaa ,
to iupacaa ,
num 28 ,
table {
255 , -- "-"
65 , -- they map directly with holes for O and J
66 ,
67 ,
68,
69,
70,
71,
72,
73,
75,
76,
77,
78,
80,
81,
82,
83,
84,
86,
87,
88,
89,
90,
85, -- U - was 88
255, -- *
79, -- O - new
74} -- J - new
}
}
} -- end of seq-code-set
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