edit

References

Nucleic acids

# BioSymbols.NucleicAcidType.

An abstract nucleic acid type.

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DNA

# BioSymbols.DNAType.

A deoxyribonucleic acid type.

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# BioSymbols.DNA_AConstant.

DNA Adenine

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# BioSymbols.DNA_CConstant.

DNA Cytosine

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# BioSymbols.DNA_GConstant.

DNA Guanine

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# BioSymbols.DNA_TConstant.

DNA Thymine

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# BioSymbols.DNA_MConstant.

DNA Adenine or Cytosine

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# BioSymbols.DNA_RConstant.

DNA Adenine or Guanine

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# BioSymbols.DNA_WConstant.

DNA Adenine or Thymine

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# BioSymbols.DNA_SConstant.

DNA Cytosine or Guanine

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# BioSymbols.DNA_YConstant.

DNA Cytosine or Thymine

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# BioSymbols.DNA_KConstant.

DNA Guanine or Thymine

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# BioSymbols.DNA_VConstant.

DNA Adenine, Cytosine or Guanine

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# BioSymbols.DNA_HConstant.

DNA Adenine, Cytosine or Thymine

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# BioSymbols.DNA_DConstant.

DNA Adenine, Guanine or Thymine

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# BioSymbols.DNA_BConstant.

DNA Cytosine, Guanine or Thymine

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# BioSymbols.DNA_NConstant.

DNA Adenine, Cytosine, Guanine or Thymine

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# BioSymbols.DNA_GapConstant.

DNA Gap

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# BioSymbols.ACGTConstant.

ACGT

Unambiguous DNA.

Examples

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

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# BioSymbols.ACGTNConstant.

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.RNAType.

A ribonucleic acid type.

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# BioSymbols.RNA_AConstant.

RNA Adenine

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# BioSymbols.RNA_CConstant.

RNA Cytosine

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# BioSymbols.RNA_GConstant.

RNA Guanine

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# BioSymbols.RNA_UConstant.

RNA Uracil

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# BioSymbols.RNA_MConstant.

RNA Adenine or Cytosine

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# BioSymbols.RNA_RConstant.

RNA Adenine or Guanine

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# BioSymbols.RNA_WConstant.

RNA Adenine or Uracil

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# BioSymbols.RNA_SConstant.

RNA Cytosine or Guanine

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# BioSymbols.RNA_YConstant.

RNA Cytosine or Uracil

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# BioSymbols.RNA_KConstant.

RNA Guanine or Uracil

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# BioSymbols.RNA_VConstant.

RNA Adenine, Cytosine or Guanine

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# BioSymbols.RNA_HConstant.

RNA Adenine, Cytosine or Uracil

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# BioSymbols.RNA_DConstant.

RNA Adenine, Guanine or Uracil

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# BioSymbols.RNA_BConstant.

RNA Cytosine, Guanine or Uracil

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# BioSymbols.RNA_NConstant.

RNA Adenine, Cytosine, Guanine or Uracil

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# BioSymbols.RNA_GapConstant.

RNA Gap

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# BioSymbols.ACGUConstant.

ACGU

Unambiguous RNA.

Examples

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

source

# BioSymbols.ACGUNConstant.

ACGUN

Unambiguous RNA and RNA_N.

Examples

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

source

Functions

# BioSymbols.alphabetMethod.

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.alphabetMethod.

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.gapMethod.

gap(DNA)

Return DNA_Gap.

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# BioSymbols.gapMethod.

gap(RNA)

Return RNA_Gap.

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# BioSymbols.complementMethod.

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.isgapMethod.

isgap(nt::NucleicAcid)

Test if nt is a gap.

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# BioSymbols.compatbitsMethod.

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.iscompatibleMethod.

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.isambiguousMethod.

isambiguous(nt::NucleicAcid)

Test if nt is an ambiguous nucleotide.

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# BioSymbols.iscertainMethod.

iscertain(nt::NucleicAcid)

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

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# BioSymbols.isGCMethod.

isGC(nt::NucleicAcid)

Test if nt is surely either guanine or cytosine.

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# BioSymbols.ispurineMethod.

ispurine(nt::NucleicAcid)

Test if nt is surely a purine.

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# BioSymbols.ispyrimidineMethod.

ispyrimidine(nt::NucleicAcid)

Test if nt is surely a pyrimidine.

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Amino acids

Amino acids

# BioSymbols.AminoAcidType.

An amino acid type.

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# BioSymbols.AA_AConstant.

Alanine

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# BioSymbols.AA_RConstant.

Arginine

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# BioSymbols.AA_NConstant.

Asparagine

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# BioSymbols.AA_DConstant.

Aspartic Acid

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# BioSymbols.AA_CConstant.

Cysteine

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# BioSymbols.AA_QConstant.

Glutamine

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# BioSymbols.AA_EConstant.

Glutamic Acid

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# BioSymbols.AA_GConstant.

Glycine

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# BioSymbols.AA_HConstant.

Histidine

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# BioSymbols.AA_IConstant.

Isoleucine

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# BioSymbols.AA_LConstant.

Leucine

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# BioSymbols.AA_KConstant.

Lysine

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# BioSymbols.AA_MConstant.

Methionine

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# BioSymbols.AA_FConstant.

Phenylalanine

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# BioSymbols.AA_PConstant.

Proline

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# BioSymbols.AA_SConstant.

Serine

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# BioSymbols.AA_TConstant.

Threonine

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# BioSymbols.AA_WConstant.

Tryptophan

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# BioSymbols.AA_YConstant.

Tyrosine

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# BioSymbols.AA_VConstant.

Valine

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# BioSymbols.AA_OConstant.

Pyrrolysine

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# BioSymbols.AA_UConstant.

Selenocysteine

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# BioSymbols.AA_BConstant.

Aspartic Acid or Asparagine

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# BioSymbols.AA_JConstant.

Leucine or Isoleucine

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# BioSymbols.AA_ZConstant.

Glutamine or Glutamic Acid

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# BioSymbols.AA_XConstant.

Unspecified or Unknown Amino Acid

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# BioSymbols.AA_TermConstant.

Terminal

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# BioSymbols.AA_GapConstant.

Amino Acid Gap

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Functions

# BioSymbols.alphabetMethod.

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.gapMethod.

gap(AminoAcid)

Return AA_Gap.

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# BioSymbols.isgapMethod.

isgap(aa::AminoAcid)

Test if aa is a gap.

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# BioSymbols.compatbitsMethod.

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.iscompatibleMethod.

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.isambiguousMethod.

isambiguous(aa::AminoAcid)

Test if aa is an ambiguous amino acid.

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# BioSymbols.iscertainMethod.

iscertain(aa::AminoAcid)

Test if aa is a non-ambiguous amino acid.

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