Biological symbols
The BioSequences module provides three biological symbol (character) types:
| Type | Meaning |
|---|---|
DNA |
DNA nucleotide |
RNA |
RNA nucleotide |
AminoAcid |
Amino 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:
| 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
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.
| NucleicAcid | Bits |
|---|---|
DNA_A, RNA_A |
0001 |
DNA_C, RNA_C |
0010 |
DNA_G, RNA_G |
0100 |
DNA_T, RNA_U |
1000 |
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:
| 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) |
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
#
BioSymbols.gap — Function.
gap(type)
Return the gap value of type.
Examples
julia> gap(DNA) DNA_Gap
#
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
#
BioSymbols.isambiguous — Function.
isambiguous(nt::NucleicAcid)
Test if nt is ambiguous nucleotide.