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References

Nucleic acids

# BioSymbols.NucleicAcid — Type.

An abstract nucleic acid type.

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DNA

# BioSymbols.DNA — Type.

A deoxyribonucleic acid type.

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# BioSymbols.DNA_A — Constant.

DNA Adenine

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# BioSymbols.DNA_C — Constant.

DNA Cytosine

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# BioSymbols.DNA_G — Constant.

DNA Guanine

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# BioSymbols.DNA_T — Constant.

DNA Thymine

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# BioSymbols.DNA_M — Constant.

DNA Adenine or Cytosine

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# BioSymbols.DNA_R — Constant.

DNA Adenine or Guanine

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# BioSymbols.DNA_W — Constant.

DNA Adenine or Thymine

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# BioSymbols.DNA_S — Constant.

DNA Cytosine or Guanine

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# BioSymbols.DNA_Y — Constant.

DNA Cytosine or Thymine

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# BioSymbols.DNA_K — Constant.

DNA Guanine or Thymine

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# BioSymbols.DNA_V — Constant.

DNA Adenine, Cytosine or Guanine

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# BioSymbols.DNA_H — Constant.

DNA Adenine, Cytosine or Thymine

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# BioSymbols.DNA_D — Constant.

DNA Adenine, Guanine or Thymine

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# BioSymbols.DNA_B — Constant.

DNA Cytosine, Guanine or Thymine

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# BioSymbols.DNA_N — Constant.

DNA Adenine, Cytosine, Guanine or Thymine

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# BioSymbols.DNA_Gap — Constant.

DNA Gap

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# BioSymbols.ACGT — Constant.

ACGT

Unambiguous DNA.

Examples

julia> ACGT
(DNA_A, DNA_C, DNA_G, DNA_T)

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# BioSymbols.ACGTN — Constant.

ACGTN

Unambiguous DNA and DNA_N.

Examples

julia> ACGTN
(DNA_A, DNA_C, DNA_G, DNA_T, DNA_N)

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RNA

# BioSymbols.RNA — Type.

A ribonucleic acid type.

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# BioSymbols.RNA_A — Constant.

RNA Adenine

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# BioSymbols.RNA_C — Constant.

RNA Cytosine

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# BioSymbols.RNA_G — Constant.

RNA Guanine

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# BioSymbols.RNA_U — Constant.

RNA Uracil

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# BioSymbols.RNA_M — Constant.

RNA Adenine or Cytosine

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# BioSymbols.RNA_R — Constant.

RNA Adenine or Guanine

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# BioSymbols.RNA_W — Constant.

RNA Adenine or Uracil

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# BioSymbols.RNA_S — Constant.

RNA Cytosine or Guanine

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# BioSymbols.RNA_Y — Constant.

RNA Cytosine or Uracil

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# BioSymbols.RNA_K — Constant.

RNA Guanine or Uracil

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# BioSymbols.RNA_V — Constant.

RNA Adenine, Cytosine or Guanine

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# BioSymbols.RNA_H — Constant.

RNA Adenine, Cytosine or Uracil

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# BioSymbols.RNA_D — Constant.

RNA Adenine, Guanine or Uracil

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# BioSymbols.RNA_B — Constant.

RNA Cytosine, Guanine or Uracil

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# BioSymbols.RNA_N — Constant.

RNA Adenine, Cytosine, Guanine or Uracil

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# BioSymbols.RNA_Gap — Constant.

RNA Gap

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# BioSymbols.ACGU — Constant.

ACGU

Unambiguous RNA.

Examples

julia> ACGU
(RNA_A, RNA_C, RNA_G, RNA_U)

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# BioSymbols.ACGUN — Constant.

ACGUN

Unambiguous RNA and RNA_N.

Examples

julia> ACGUN
(RNA_A, RNA_C, RNA_G, RNA_U, RNA_N)

source

Functions

# BioSymbols.alphabet — Method.

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

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# BioSymbols.alphabet — Method.

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

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# BioSymbols.gap — Method.

gap(DNA)

Return DNA_Gap.

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# BioSymbols.gap — Method.

gap(RNA)

Return RNA_Gap.

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# BioSymbols.complement — Method.

complement(nt::NucleicAcid)

Return the complementary nucleotide of nt.

This function returns the union of all possible complementary nucleotides.

Examples

julia> complement(DNA_A)
DNA_T

julia> complement(DNA_N)
DNA_N

julia> complement(RNA_U)
RNA_A

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# BioSymbols.isgap — Method.

isgap(nt::NucleicAcid)

Test if nt is a gap.

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# BioSymbols.compatbits — Method.

compatbits(nt::NucleicAcid)

Return the compatibility bits of nt as UInt8.

Examples

julia> compatbits(DNA_A)
0x01

julia> compatbits(DNA_C)
0x02

julia> compatbits(DNA_N)
0x0f

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# BioSymbols.iscompatible — Method.

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

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# BioSymbols.isambiguous — Method.

isambiguous(nt::NucleicAcid)

Test if nt is an ambiguous nucleotide.

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# BioSymbols.iscertain — Method.

iscertain(nt::NucleicAcid)

Test if nt is a non-ambiguous nucleotide e.g. ACGT.

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# BioSymbols.isGC — Method.

isGC(nt::NucleicAcid)

Test if nt is surely either guanine or cytosine.

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# BioSymbols.ispurine — Method.

ispurine(nt::NucleicAcid)

Test if nt is surely a purine.

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# BioSymbols.ispyrimidine — Method.

ispyrimidine(nt::NucleicAcid)

Test if nt is surely a pyrimidine.

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Amino acids

# BioSymbols.AminoAcid — Type.

An amino acid type.

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# BioSymbols.AA_A — Constant.

Alanine

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# BioSymbols.AA_R — Constant.

Arginine

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# BioSymbols.AA_N — Constant.

Asparagine

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# BioSymbols.AA_D — Constant.

Aspartic Acid

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# BioSymbols.AA_C — Constant.

Cysteine

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# BioSymbols.AA_Q — Constant.

Glutamine

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# BioSymbols.AA_E — Constant.

Glutamic Acid

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# BioSymbols.AA_G — Constant.

Glycine

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# BioSymbols.AA_H — Constant.

Histidine

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# BioSymbols.AA_I — Constant.

Isoleucine

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# BioSymbols.AA_L — Constant.

Leucine

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# BioSymbols.AA_K — Constant.

Lysine

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# BioSymbols.AA_M — Constant.

Methionine

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# BioSymbols.AA_F — Constant.

Phenylalanine

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# BioSymbols.AA_P — Constant.

Proline

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# BioSymbols.AA_S — Constant.

Serine

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# BioSymbols.AA_T — Constant.

Threonine

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# BioSymbols.AA_W — Constant.

Tryptophan

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# BioSymbols.AA_Y — Constant.

Tyrosine

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# BioSymbols.AA_V — Constant.

Valine

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# BioSymbols.AA_O — Constant.

Pyrrolysine

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# BioSymbols.AA_U — Constant.

Selenocysteine

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# BioSymbols.AA_B — Constant.

Aspartic Acid or Asparagine

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# BioSymbols.AA_J — Constant.

Leucine or Isoleucine

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# BioSymbols.AA_Z — Constant.

Glutamine or Glutamic Acid

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# BioSymbols.AA_X — Constant.

Unspecified or Unknown Amino Acid

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# BioSymbols.AA_Term — Constant.

Terminal

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# BioSymbols.AA_Gap — Constant.

Amino Acid Gap

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Functions

# BioSymbols.alphabet — Method.

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

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# BioSymbols.gap — Method.

gap(AminoAcid)

Return AA_Gap.

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# BioSymbols.isgap — Method.

isgap(aa::AminoAcid)

Test if aa is a gap.

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# BioSymbols.compatbits — Method.

compatbits(aa::AminoAcid)

Return the compatibility bits of aa as UInt32.

Examples

julia> compatbits(AA_A)
0x00000001

julia> compatbits(AA_J)
0x00000600

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# BioSymbols.iscompatible — Method.

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

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# BioSymbols.isambiguous — Method.

isambiguous(aa::AminoAcid)

Test if aa is an ambiguous amino acid.

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# BioSymbols.iscertain — Method.

iscertain(aa::AminoAcid)

Test if aa is a non-ambiguous amino acid.

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