Biological symbols

The BioSequences module reexports the biological symbol (character) types that are provided by BioSymbols.jl:

Type	Meaning
`DNA`	DNA nucleotide
`RNA`	RNA nucleotide
`AminoAcid`	Amino acid

These symbols are elements of biological sequence types, just as characters are elements of strings.

DNA and RNA nucleotides

The set of nucleotide symbols in BioSequences covers the IUPAC nucleotide bases plus a gap symbol:

Symbol	Constant	Meaning
'A'	`DNA_A` / `RNA_A`	A; Adenine
'C'	`DNA_C` / `RNA_C`	C; Cytosine
'G'	`DNA_G` / `RNA_G`	G; Guanine
'T'	`DNA_T`	T; Thymine (DNA only)
'U'	`RNA_U`	U; Uracil (RNA only)
'M'	`DNA_M` / `RNA_M`	A or C
'R'	`DNA_R` / `RNA_R`	A or G
'W'	`DNA_W` / `RNA_W`	A or T/U
'S'	`DNA_S` / `RNA_S`	C or G
'Y'	`DNA_Y` / `RNA_Y`	C or T/U
'K'	`DNA_K` / `RNA_K`	G or T/U
'V'	`DNA_V` / `RNA_V`	A or C or G; not T/U
'H'	`DNA_H` / `RNA_H`	A or C or T; not G
'D'	`DNA_D` / `RNA_D`	A or G or T/U; not C
'B'	`DNA_B` / `RNA_B`	C or G or T/U; not A
'N'	`DNA_N` / `RNA_N`	A or C or G or T/U
'-'	`DNA_Gap` / `RNA_Gap`	Gap (none of the above)

https://www.bioinformatics.org/sms/iupac.html

Symbols are accessible as constants with DNA_ or RNA_ prefix:

julia> DNA_A
DNA_A

julia> DNA_T
DNA_T

julia> RNA_U
RNA_U

julia> DNA_Gap
DNA_Gap

julia> typeof(DNA_A)
DNA

julia> typeof(RNA_A)
RNA

Symbols can be constructed by converting regular characters:

julia> convert(DNA, 'C')
DNA_C

julia> convert(DNA, 'C') === DNA_C
true

Amino acids

The set of amino acid symbols also covers the IUPAC amino acid symbols plus a gap symbol:

Symbol	Constant	Meaning
'A'	`AA_A`	Alanine
'R'	`AA_R`	Arginine
'N'	`AA_N`	Asparagine
'D'	`AA_D`	Aspartic acid (Aspartate)
'C'	`AA_C`	Cysteine
'Q'	`AA_Q`	Glutamine
'E'	`AA_E`	Glutamic acid (Glutamate)
'G'	`AA_G`	Glycine
'H'	`AA_H`	Histidine
'I'	`AA_I`	Isoleucine
'L'	`AA_L`	Leucine
'K'	`AA_K`	Lysine
'M'	`AA_M`	Methionine
'F'	`AA_F`	Phenylalanine
'P'	`AA_P`	Proline
'S'	`AA_S`	Serine
'T'	`AA_T`	Threonine
'W'	`AA_W`	Tryptophan
'Y'	`AA_Y`	Tyrosine
'V'	`AA_V`	Valine
'O'	`AA_O`	Pyrrolysine
'U'	`AA_U`	Selenocysteine
'B'	`AA_B`	Aspartic acid or Asparagine
'J'	`AA_J`	Leucine or Isoleucine
'Z'	`AA_Z`	Glutamine or Glutamic acid
'X'	`AA_X`	Any amino acid
'*'	`AA_Term`	Termination codon
'-'	`AA_Gap`	Gap (none of the above)

https://www.bioinformatics.org/sms/iupac.html

Symbols are accessible as constants with AA_ prefix:

julia> AA_A
AA_A

julia> AA_Q
AA_Q

julia> AA_Term
AA_Term

julia> typeof(AA_A)
AminoAcid

Symbols can be constructed by converting regular characters:

julia> convert(AminoAcid, 'A')
AA_A

julia> convert(AminoAcid, 'P') === AA_P
true

Other functions

BioSymbols.alphabet — Function

alphabet(DNA)

Get all symbols of DNA in sorted order.

Examples

julia> alphabet(DNA)
(DNA_Gap, DNA_A, DNA_C, DNA_M, DNA_G, DNA_R, DNA_S, DNA_V, DNA_T, DNA_W, DNA_Y, DNA_H, DNA_K, DNA_D, DNA_B, DNA_N)

julia> issorted(alphabet(DNA))
true

source

alphabet(RNA)

Get all symbols of RNA in sorted order.

Examples

julia> alphabet(RNA)
(RNA_Gap, RNA_A, RNA_C, RNA_M, RNA_G, RNA_R, RNA_S, RNA_V, RNA_U, RNA_W, RNA_Y, RNA_H, RNA_K, RNA_D, RNA_B, RNA_N)

julia> issorted(alphabet(RNA))
true

source

alphabet(AminoAcid)

Get all symbols of AminoAcid in sorted order.

Examples

julia> alphabet(AminoAcid)
(AA_A, AA_R, AA_N, AA_D, AA_C, AA_Q, AA_E, AA_G, AA_H, AA_I, AA_L, AA_K, AA_M, AA_F, AA_P, AA_S, AA_T, AA_W, AA_Y, AA_V, AA_O, AA_U, AA_B, AA_J, AA_Z, AA_X, AA_Term, AA_Gap)

julia> issorted(alphabet(AminoAcid))
true

source

BioSymbols.gap — Function

gap(::Type{T})::T

Return the gap (indel) representation of T. By default, gap is defined for DNA, RNA, AminoAcid and Char.

Examples

julia> gap(RNA)
RNA_Gap

julia> gap(Char)
'-': ASCII/Unicode U+002D (category Pd: Punctuation, dash)

source

BioSymbols.iscompatible — Function

iscompatible(x::S, y::S) where S <: BioSymbol

Test if x and y are compatible with each other.

Examples

julia> iscompatible(AA_A, AA_R)
false

julia> iscompatible(AA_A, AA_X)
true

julia> iscompatible(DNA_A, DNA_A)
true

julia> iscompatible(DNA_C, DNA_N)  # DNA_N can be DNA_C
true

julia> iscompatible(DNA_C, DNA_R)  # DNA_R (A or G) cannot be DNA_C
false

source

BioSymbols.isambiguous — Function

isambiguous(nt::NucleicAcid)

Test if nt is an ambiguous nucleotide.

source

isambiguous(aa::AminoAcid)

Test if aa is an ambiguous amino acid.

source