Biological Symbols

Biological symbols

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

TypeMeaning
DNADNA nucleotide
RNARNA nucleotide
AminoAcidAmino acid

These symbols are elements of biological sequences, just as characters are elements of strings. See sections beginning from Introduction to the sequence data-types section for details.

DNA and RNA nucleotides

Set of nucleotide symbols in BioSequences.jl covers IUPAC nucleotide base plus a gap symbol:

SymbolConstantMeaning
'A'DNA_A / RNA_AA; Adenine
'C'DNA_C / RNA_CC; Cytosine
'G'DNA_G / RNA_GG; Guanine
'T'DNA_TT; Thymine (DNA only)
'U'RNA_UU; Uracil (RNA only)
'M'DNA_M / RNA_MA or C
'R'DNA_R / RNA_RA or G
'W'DNA_W / RNA_WA or T/U
'S'DNA_S / RNA_SC or G
'Y'DNA_Y / RNA_YC or T/U
'K'DNA_K / RNA_KG or T/U
'V'DNA_V / RNA_VA or C or G; not T/U
'H'DNA_H / RNA_HA or C or T; not G
'D'DNA_D / RNA_DA or G or T/U; not C
'B'DNA_B / RNA_BC or G or T/U; not A
'N'DNA_N / RNA_NA or C or G or T/U
'-'DNA_Gap / RNA_GapGap (none of the above)

http://www.insdc.org/documents/feature_table.html#7.4.1

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)
BioSymbols.DNA

julia> typeof(RNA_A)
BioSymbols.RNA

Symbols can be constructed by converting regular characters:

julia> convert(DNA, 'C')
DNA_C

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

Every nucleotide is encoded using the lower 4 bits of a byte. An unambiguous nucleotide has only one set bit and the other bits are unset. The table below summarizes all unambiguous nucleotides and their corresponding bits. An ambiguous nucleotide is the bitwise OR of unambiguous nucleotides that the ambiguous nucleotide can take. For example, DNA_R (meaning the nucleotide is either DNA_A or DNA_G) is encoded as 0101 because 0101 is the bitwise OR of 0001 (DNA_A) and 0100 (DNA_G). The gap symbol is always 0000.

NucleicAcidBits
DNA_A, RNA_A0001
DNA_C, RNA_C0010
DNA_G, RNA_G0100
DNA_T, RNA_U1000

The next examples demonstrate bit operations of DNA:

julia> bits(reinterpret(UInt8, DNA_A))
"00000001"

julia> bits(reinterpret(UInt8, DNA_G))
"00000100"

julia> bits(reinterpret(UInt8, DNA_R))
"00000101"

julia> bits(reinterpret(UInt8, DNA_B))
"00001110"

julia> ~DNA_A
DNA_B

julia> DNA_A | DNA_G
DNA_R

julia> DNA_R & DNA_B
DNA_G

Amino acids

Set of amino acid symbols also covers IUPAC amino acid symbols plus a gap symbol:

SymbolConstantMeaning
'A'AA_AAlanine
'R'AA_RArginine
'N'AA_NAsparagine
'D'AA_DAspartic acid (Aspartate)
'C'AA_CCysteine
'Q'AA_QGlutamine
'E'AA_EGlutamic acid (Glutamate)
'G'AA_GGlycine
'H'AA_HHistidine
'I'AA_IIsoleucine
'L'AA_LLeucine
'K'AA_KLysine
'M'AA_MMethionine
'F'AA_FPhenylalanine
'P'AA_PProline
'S'AA_SSerine
'T'AA_TThreonine
'W'AA_WTryptophan
'Y'AA_YTyrosine
'V'AA_VValine
'O'AA_OPyrrolysine
'U'AA_USelenocysteine
'B'AA_BAspartic acid or Asparagine
'J'AA_JLeucine or Isoleucine
'Z'AA_ZGlutamine or Glutamic acid
'X'AA_XAny amino acid
'*'AA_TermTermination codon
'-'AA_GapGap (none of the above)

http://www.insdc.org/documents/feature_table.html#7.4.3

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)
BioSymbols.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.alphabetFunction.
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

Gets the alphabet encoding of a given BioSequence.

source
BioSymbols.gapFunction.
gap(DNA)

Return DNA_Gap.

source
gap(RNA)

Return RNA_Gap.

source
gap(AminoAcid)

Return AA_Gap.

source
iscompatible(x::T, y::T) where T <: NucleicAcid

Test if x and y are compatible with each other (i.e. x and y can be the same symbol).

x and y must be the same type.

Examples

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
iscompatible(x::AminoAcid, y::AminoAcid)

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
source
isambiguous(nt::NucleicAcid)

Test if nt is an ambiguous nucleotide.

source
isambiguous(aa::AminoAcid)

Test if aa is an ambiguous amino acid.

source