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Maybe and Exact Filters

Maybe

This filter is true iff its child expression is true, where, for all NucleotideEquals or AminoAcidEquals expressions contained in this filters subtree, there exists at least one possible non-ambiguous sequence symbols at the sequence position, where the expression would evaluate to true.

Exact

This filter is true iff its child expression is true, where, for all NucleotideEquals or AminoAcidEquals expressions contained in this filters subtree, the expression would evaluate to true for all possible non-ambiguous sequence symbols at the sequence position.

Ambiguity Symbol Graph

Ambiguous symbols are IUPAC codes that represent multiple possible concrete symbols. Two maps define the ambiguity system:

  • CODES_FOR[S]: The set of concrete symbols that S codes for (the primary definition).
  • AMBIGUITY_SYMBOLS[S]: The set of all symbols Y such that CODES_FOR[S] ⊆ CODES_FOR[Y]. In other words, all symbols that are at least as general as S. This is derived from CODES_FOR.

Nucleotide CODES_FOR Graph

Symbol -> Codes for
───────────────────────────────
GAP    -> {GAP}
A      -> {A}
C      -> {C}
G      -> {G}
T      -> {T}
R      -> {A, G}           (puRine)
Y      -> {C, T}           (pYrimidine)
S      -> {G, C}           (Strong)
W      -> {A, T}           (Weak)
K      -> {G, T}           (Keto)
M      -> {A, C}           (aMino)
B      -> {C, G, T}        (not A)
D      -> {A, G, T}        (not C)
H      -> {A, C, T}        (not G)
V      -> {A, C, G}        (not T)
N      -> {all symbols}    (aNy)

Nucleotide AMBIGUITY_SYMBOLS (derived)

Symbol -> Matched by
───────────────────────────────
GAP    -> {GAP, N}
A      -> {A, R, M, W, D, H, V, N}
C      -> {C, Y, S, M, B, H, V, N}
G      -> {G, R, K, S, B, D, V, N}
T      -> {T, Y, K, W, B, D, H, N}
R      -> {R, D, V, N}
Y      -> {Y, B, H, N}
S      -> {S, B, V, N}
W      -> {W, D, H, N}
K      -> {K, B, D, N}
M      -> {M, H, V, N}
B      -> {B, N}
D      -> {D, N}
H      -> {H, N}
V      -> {V, N}
N      -> {N}

Amino Acid CODES_FOR Graph

Symbol -> Codes for
───────────────────────────────
GAP    -> {GAP}
A      -> {A}              (Alanine)
C      -> {C}              (Cysteine)
D      -> {D}              (Aspartic Acid)
E      -> {E}              (Glutamic Acid)
F      -> {F}              (Phenylalanine)
G      -> {G}              (Glycine)
H      -> {H}              (Histidine)
I      -> {I}              (Isoleucine)
K      -> {K}              (Lysine)
L      -> {L}              (Leucine)
M      -> {M}              (Methionine)
N      -> {N}              (Asparagine)
O      -> {O}              (Pyrrolysine)
P      -> {P}              (Proline)
Q      -> {Q}              (Glutamine)
R      -> {R}              (Arginine)
S      -> {S}              (Serine)
T      -> {T}              (Threonine)
U      -> {U}              (Selenocysteine)
V      -> {V}              (Valine)
W      -> {W}              (Tryptophan)
Y      -> {Y}              (Tyrosine)
B      -> {D, N}           (Aspartic acid or Asparagine)
J      -> {L, I}           (Leucine or Isoleucine)
Z      -> {Q, E}           (Glutamine or Glutamic acid)
STOP   -> {STOP}
X      -> {all symbols}    (any amino acid)

Amino Acid AMBIGUITY_SYMBOLS (derived)

Symbol -> Matched by
───────────────────────────────
GAP    -> {GAP, X}
A      -> {A, X}
C      -> {C, X}
D      -> {D, B, X}
E      -> {E, Z, X}
F      -> {F, X}
G      -> {G, X}
H      -> {H, X}
I      -> {I, J, X}
K      -> {K, X}
L      -> {L, J, X}
M      -> {M, X}
N      -> {N, B, X}
O      -> {O, X}
P      -> {P, X}
Q      -> {Q, Z, X}
R      -> {R, X}
S      -> {S, X}
T      -> {T, X}
U      -> {U, X}
V      -> {V, X}
W      -> {W, X}
Y      -> {Y, X}
B      -> {B, X}
J      -> {J, X}
Z      -> {Z, X}
STOP   -> {STOP, X}
X      -> {X}