-- This is the set of NCBI sequence code tables -- 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 "", name "" }, { symbol "K", name "Lysine" }, { symbol "L", name "Leucine" }, { symbol "M", name "Methionine" }, { symbol "N", name "Asparagine" } , { symbol "", name "" }, { symbol "P", name "Proline" }, { symbol "Q", name "Glutamine"}, { symbol "R", name "Arginine"}, { symbol "S", name "Serine"}, { symbol "T", name "Threonine"}, { symbol "", name ""}, { 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 "", name "" }, { symbol "K", name "Lysine" }, { symbol "L", name "Leucine" }, { symbol "M", name "Methionine" }, { symbol "N", name "Asparagine" } , { symbol "", name "" }, { 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 26 , -- continuous 0-25 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" } } -- end of table } , { -- NCBIstdaa code ncbistdaa , num 26 , -- continuous 0-25 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 } -- 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, 255, -- J 75, 76, 77, 78, 255, -- O 80, 81, 82, 83, 84, 255, -- U 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, 255, -- J 75, 76, 77, 78, 255, -- O 80, 81, 82, 83, 84, 88, -- U -> X 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, 255, -- J 10, 11, 12, 13, 255, -- O 14, 15, 16, 17, 18, 255, -- U 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, 255, -- J 10, 11, 12, 13, 255, -- O 14, 15, 16, 17, 18, 24, -- U 19, 20, 21, 22, 23 } } , { from ncbistdaa , to ncbieaa , num 26 , 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} -- * } , { from ncbistdaa , to iupacaa , num 26 , 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, 88, -- U 255} -- * } } } -- end of seq-code-set