Nucleic Acids
Type definitions
BioSymbols provides two types of nucleic acids:
| Type | Meaning |
|---|---|
DNA | deoxyribonucleic acid |
RNA | ribonucleic acid |
These two are an 8-bit primitive type and a subtype of NucleicAcid.
julia> sizeof(DNA)
1
julia> DNA <: NucleicAcid
true
The set of nucleotide symbols in BioSymbols.jl covers the IUPAC nucleotides as well as 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) |
http://www.insdc.org/documents/feature_table.html#7.4.1
These 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
julia> convert(DNA, 'c') === convert(DNA, 'C') # convertion is not case-sensitive
true
print and show methods are defined to output the text representation of a symbol:
julia> print(DNA_A) # un-decorated text
A
julia> show(DNA_A) # informative text
DNA_ABit encoding
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.
julia> bitstring(reinterpret(UInt8, DNA_A))
"00000001"
julia> bitstring(reinterpret(UInt8, DNA_G))
"00000100"
julia> bitstring(reinterpret(UInt8, DNA_R))
"00000101"
This bit encoding enables efficient bit operations:
julia> DNA_A | DNA_G # A or G
DNA_R
julia> DNA_A & DNA_G # A and G
DNA_Gap
julia> DNA_A | ~DNA_A # A or not A
DNA_N
julia> DNA_A | DNA_C | DNA_G | DNA_T # any DNA
DNA_N