Biological symbols

The Bio.Seq module provides three biological symbol (character) types:

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 Bio.jl covers IUPAC nucleotide base plus a gap symbol:

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.

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:

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.alphabet — Function.

alphabet(type)

Get all symbols of type.

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

# BioSymbols.gap — Function.

gap(type)

Return the gap value of type.

Examples

julia> gap(DNA)
DNA_Gap

source

# BioSymbols.iscompatible — Function.

iscompatible(x, y)

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 (DNA, RNA or AminoAcid).

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

julia> iscompatible(AA_A, AA_X)    # AA_X can be AA_A
true

source

# BioSymbols.isambiguous — Function.

isambiguous(nt::NucleicAcid)

Test if nt is ambiguous nucleotide.

source