X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FGeneticCodes.dat;fp=resources%2FGeneticCodes.dat;h=4a739b7149c8442133a143fcc0d06700b1c4c951;hb=a97dbd3e6e9707de13f47c66beaa15df8ea24d0e;hp=0000000000000000000000000000000000000000;hpb=7ef3d2f322e86a39a4cf8df7793b434a4d028488;p=jalview.git

diff --git a/resources/GeneticCodes.dat b/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	# *