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basicdata.yml
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basicdata.yml
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---
##############################################
# definition of datatypes in YAML format #
# Copyright (c) 2018 by Bui Quang Minh #
##############################################
### DNA data definition ###
- datatype: DNA
state: &Nucleotide [ A, C, G, T ] # anchor to Nucleotide
missing: &NTmissing [ N, "?" ]
gap: &NTgap "-"
equate:
U: T # T and U are the same
R: [A, G] # R is interpreted as A or G
Y: [C, T]
W: [A, T]
S: [G, C]
M: [A, C]
K: [G, T]
B: [C, G, T]
H: [A, C, T]
D: [A, G, T]
V: [A, G, C]
### Amino-acid data definition ###
- datatype: AA
state: [ A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V ]
missing: [ X, "?", "*" ]
gap: "-"
equate:
B: [ N, D ]
Z: [ Q, E ]
J: [ I, L ]
### Binary (0/1) data ###
- datatype: BIN
state: [ 0, 1 ]
missing: "?"
gap: "-"
### RY data definition ###
- datatype: RY
state: [ R, Y ] # R=AG, Y=CT
missing: [ N, "?", W, S, M, K, B, H, D, V ]
gap: "-"
equate:
A: R
C: Y
G: R
T: Y
U: Y
### Morphological data ###
- datatype: MORPH
state: [ 0..9, A..Z ]
missing: "?"
gap: "-"
### Codon data with standard genetic code ###
- datatype: CODON
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: [ K, N, K, N, T, T, T, T, R, S, R, S, I, I, M, I,
Q, H, Q, H, P, P, P, P, R, R, R, R, L, L, L, L,
E, D, E, D, A, A, A, A, G, G, G, G, V, V, V, V,
X, Y, X, Y, S, S, S, S, X, C, W, C, L, F, L, F ]
### Codon data with Vertebrate Mitochondrial code ###
- datatype: CODON2
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTT*S*SMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Yeast Mitochondrial code ###
- datatype: CODON3
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSMIMIQHQHPPPPRRRRTTTTEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Mold, Protozoan code ###
- datatype: CODON4
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Invertebrate Mitochondrial code ###
- datatype: CODON5
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Ciliate, Dasycladacean and Hexamita Nuclear code ###
- datatype: CODON6
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSS*CWCLFLF
### Codon data with Echinoderm and Flatworm Mitochondrial code ###
- datatype: CODON9
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Euplotid Nuclear code ###
- datatype: CODON10
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSCCWCLFLF
### Codon data with Bacterial, Archaeal and Plant Plastid code ###
- datatype: CODON11
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF
### Codon data with Alternative Yeast Nuclear code ###
- datatype: CODON12
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLSLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF
### Codon data with Ascidian Mitochondrial code ###
- datatype: CODON13
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTGSGSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Alternative Flatworm Mitochondrial code ###
- datatype: CODON14
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVYY*YSSSSWCWCLFLF
### Codon data with Blepharisma Nuclear code ###
- datatype: CODON15
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YQYSSSS*CWCLFLF
### Codon data with Chlorophycean Mitochondrial code ###
- datatype: CODON16
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLYSSSS*CWCLFLF
### Codon data with Trematode Mitochondrial code ###
- datatype: CODON21
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: NNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Scenedesmus obliquus mitochondrial code ###
- datatype: CODON22
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLY*SSS*CWCLFLF
### Codon data with Thraustochytrium Mitochondrial code ###
- datatype: CODON23
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWC*FLF
### Codon data with Pterobranchia mitochondrial code ###
- datatype: CODON24
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTSSKSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF
### Codon data with Candidate Division SR1 and Gracilibacteria code ###
- datatype: CODON25
state: [ *Nucleotide, *Nucleotide, *Nucleotide ] # reference to Nucleotide
missing: [ *NTmissing, *NTmissing, *NTmissing ]
gap: [ *NTgap, *NTgap, *NTgap ]
translate: KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSGCWCLFLF