• BioVossEncoder.VossEncoder
• BioVossEncoder.pfm
• BioVossEncoder.vossmatrix
• BioVossEncoder.vossvector

BioVossEncoder.VossEncoder Type

struct VossEncoder{A<:NucleicAcidAlphabet, B<:BitMatrix}

The VossEncoder struct represents a binary matrix encoding a sequence of nucleic acids. This is also called the Voss representation of a sequence.

Fields

• alphabet::A: The nucleic acid alphabet used for encoding.

• bitmatrix::B: The binary matrix representing the encoded sequence.

Constructors

• VossEncoder(sequence::SeqOrView{A}): Constructs a VossEncoder from a sequence of nucleic acids.

Arguments

• sequence::SeqOrView{A}: The sequence of nucleic acids to be encoded.

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BioVossEncoder.pfm Method

pfm(v::Vector{T}) where {T <: SeqOrView{<:Alphabet}}

Calculate the position frequency matrix (PFM) for a given vector of sequences or sequence views.

Arguments

• v::Vector{T}: A vector of sequences or sequence views, where each element is of type T which is a subtype of SeqOrView parameterized by an Alphabet.

Returns

• A matrix representing the position frequency matrix (PFM) of the input sequences.

Details

• The function first creates a copy of the input vector v.

• It then determines the sequence with the maximum length (vmax) and removes it from the vector.

• The function computes the Voss matrix for each sequence in the vector.

• Finally, it sums the Voss matrices and returns the result as the position frequency matrix.

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BioVossEncoder.vossmatrix Method

vossmatrix(VossEncoder::VossEncoder{A, B}) where {A <: NucleicAcidAlphabet, B <: BitMatrix}
vossmatrix(seq::NucleicSeqOrView{A}) where {A <: NucleicAcidAlphabet}
vossmatrix(seq::SeqOrView{AminoAcidAlphabet}) where {A <: AminoAcidAlphabet}

Create a binary sequence matrix from a given nucleic acid sequence.

Arguments

• sequence: A nucleic acid sequence.

Returns

The binary sequence matrix.

Examples

julia> vossmatrix(aa"IANRMWRDTIED")

    20×12 BitMatrix:
    0  1  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  1  0  0  0  1
    0  0  0  0  0  0  0  0  0  0  1  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    1  0  0  0  0  0  0  0  0  1  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  1  0  0  0  0  0  0  0
    0  0  1  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  1  0  0  1  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  1  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  1  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0

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BioVossEncoder.vossvector Method

vossvector(seq::NucleicSeqOrView{A}, molecule::T) where {A <: NucleicAcidAlphabet, T <: BioSymbol}
vossvector(seq::SeqOrView{AminoAcidAlphabet}, molecule::T) where {T <: BioSymbol}
vossvector(seq::SeqOrView{A}, molecules::Tuple{Vararg{T}}) where {A <: Alphabet, T <: BioSymbol}

Converts a sequence of nucleotides into a binary representation.

Arguments

• seq::SeqOrView{A}: The input sequence of nucleotides.

• molecule::BioSymbol: The nucleotide to be encoded as 1, while others are encoded as 0.

• molecules::Tuple{Vararg{T}}: The nucleotides to be encoded as 1, while others are encoded as 0.

Returns

A BitVector representing the binary encoding of the input sequence, where 1 indicates the presence of the specified nucleotide and 0 indicates the absence in the ith position of the sequence.

Examples

julia> vossvector(dna"ACGT", DNA_A)

    4-element view(::BitMatrix, 1, :) with eltype Bool:
     1
     0
     0
     0

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