JAL-2620 alternative genetic code translation tables

[jalview.git] / resources / GeneticCodes.dat

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+#
+# Genetic code translation tables
+# Standard code comes first
+# Other codes only list deviations from the standard
+# Columns are tab separated
+# source: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi (July 2017)
+#
+Ambiguity Codes
+R      AG
+Y      TC
+W      AT
+S      GC
+M      AC
+K      GT
+H      ATC
+B      GTC
+V      GAC
+D      GAT
+N      GATC
+Table  1       Standard
+AAA    K
+AAG    K
+AAC    N
+AAT    N
+CAA    Q
+CAG    Q
+CAC    H
+CAT    H
+GAA    E
+GAG    E
+GAC    D
+GAT    D
+TAC    Y
+TAT    Y
+ACA    T
+ACC    T
+ACT    T
+ACG    T
+CCA    P
+CCG    P
+CCC    P
+CCT    P
+GCA    A
+GCG    A
+GCC    A
+GCT    A
+TCA    S
+TCG    S
+TCC    S
+TCT    S
+AGC    S
+AGT    S
+AGA    R
+AGG    R
+CGA    R
+CGG    R
+CGC    R
+CGT    R
+GGA    G
+GGG    G
+GGC    G
+GGT    G
+TGA    *
+TAA    *
+TAG    *
+TGG    W
+TGC    C
+TGT    C
+ATA    I
+ATC    I
+ATT    I
+ATG    M
+CTA    L
+CTG    L
+CTC    L
+CTT    L
+TTA    L
+TTG    L
+GTA    V
+GTG    V
+GTC    V
+GTT    V
+TTC    F
+TTT    F
+Table  2       Vertebrate Mitochondrial
+AGA    *       # R
+AGG    *       # R
+ATA    M       # I
+TGA    W       # *
+Table  3       Yeast Mitochondrial
+ATA    M       # I
+CTT    T       # L
+CTC    T       # L
+CTA    T       # L
+CTG    T       # L
+TGA    W       # *
+Table  4       Mold, Protozoan, and Coelenterate Mitochondrial
+TGA    W       # *
+Table  5       Invertebrate Mitochondrial
+AGA    S       # R
+AGG    S       # R
+ATA    M       # I
+TGA    W       # *
+Table  6       Ciliate, Dasycladacean and Hexamita Nuclear
+TAA    Q       # *
+TAG    Q       # * 
+Table  9       Echinoderm and Flatworm Mitochondrial
+AAA    N       # K
+AGA    S       # R
+AGG    S       # R
+TGA    W       # *
+Table  10      Euplotid Nuclear
+TGA    C       #  *
+Table  11      Bacterial, Archaeal and Plant Plastid
+Table  12      Alternative Yeast Nuclear
+CTG    S       # L
+Table  13      Ascidian Mitochondrial
+AGA    G       # R
+AGG    G       # R
+ATA    M       # I
+TGA    W       # *
+Table  14      Alternative Flatworm Mitochondrial
+AAA    N       # K
+AGA    S       # R
+AGG    S       # R
+TAA    Y       # *
+TGA    W       # *
+Table  16      Chlorophycean Mitochondrial
+TAG    L       # *
+Table  21      Trematode Mitochondrial
+TGA    W       # *
+ATA    M       # I
+AGA    S       # R
+AGG    S       # R
+AAA    N       # K
+Table  22      Scenedesmus obliquus Mitochondrial
+TCA    *       # S
+TAG    L       # *
+Table  23      Thraustochytrium Mitochondrial
+TTA    *       # L
+Table  24      Pterobranchia Mitochondrial
+AGA    S       # R
+AGG    K       # R
+TGA    W       # *
+Table  25      Candidate Division SR1 and Gracilibacteria 
+TGA    G       # *
+Table  26      Pachysolen tannophilus Nuclear
+CTG    A       # L
+Table  27      Karyorelict Nuclear
+TAG    Q       # *
+TAA    Q       # *
+TGA    W       # or STOP       # * 
+Table  28      Condylostoma Nuclear
+TAA    Q       # or STOP       # *
+TAG    Q       # or STOP       # *
+TGA    W       # or STOP       # *
+Table  29      Mesodinium Nuclear
+TAA    Y       # *
+TAG    Y       # *
+Table  30      Peritrich Nuclear
+TAA    E       # *
+TAG    E       # *
+Table  31      Blastocrithidia Nuclear
+TGA    W       # *
+TAG    E       # or STOP       # * 
+TAA    E       # or STOP       # *