Types

This page describes the core types that are used in the Package. These types are used for repesent dna sequences, alignment movement options and scoring of alignments. For reference the core type are presented below

Core Types

• Move - represents an allowed alignment move during alignment (e.g. insert gap, or match nucleotide)

• MoveSet - represents a collection of Move objects

• ScoreScheme - represents how different aspects of an alignment is scored (e.g. substitution penalty, extension penalty)

• LongDNA{4} - represents the dna sequences. See LongDNA in the BioSequences.jl documentation.

In this document we outline in-depth how the Move, MoveSet and ScoreScheme types work. For documentation on LongDNA{4} we recommend looking at the documentation from [BioSequences.jl].

Move

Represents a single allowed move during alignment (e.g., a match, insertion, or deletion). Moves can preserve codon reading frames by aligning phases.

Move(
    step::Int, 
    score::Float64,         
    horizontal_stride::Int, 
    horizontal_phase::Int,  
    vertical_stride::Int,   
    vertical_phase::Int,
    extensionAble::Bool
)

Fields

• step::Int: How many alignment matrix steps this move advances. E.g. a move could correspond to a gap of length 1 or a gap of lenth 3.

• score::Float64: The cost (or negative score) for using this move once in an alignment. If a Move has a high score it will be used less in the optimal alignment.

• horizontal_stride::Int: Bases consumed from the reference sequence.

• horizontal_phase::Int: Frame offset in the reference (top sequence).

• vertical_stride::Int: Bases consumed from the query sequence.

• vertical_phase::Int: Frame offset in the query (bottom sequence).

• extensionAble::Bool: Whether this move can be extended (e.g., in gap extension scoring).

The stride and phase fields are what enable us to make some moves Codon-preserving.

Constructors

For convenience, there are a few constructors:

# keyword constructor
Move(; step::Int, score::Float64, stride::Int, phase::Int, extensionAble::Bool=false)
# 
Move(step, score, stride, phase, extensionAble=false)
# ignore stide and phase considerations by letting stride = 1, phase = 0
Move(step, score, extensionAble=false)

MoveSet

A MoveSet groups together the allowable match, insertion, and deletion moves used in dynamic programming.

MoveSet(
    match_moves::Vector{Move},
    hor_moves::Vector{Move},
    vert_moves::Vector{Move}
)

Fields

• match_moves: Moves that align bases from both sequences (e.g., match/mismatch).
• hor_moves: Gaps in the reference sequence (insertions).
• vert_moves: Gaps in the query sequence (deletions).

Example

The default codon-aware move set is provided by:

std_codon_moveset()

An example for a custom moveset is given by

match_moves = [Move(1,.0)]
hor_moves =  [Move(1, 2.0, 1, 0, 1,0, false), Move(3, 2.0, 1,0,3,0, true)]
vert_moves = [Move(1, 2.0, 1, 0, 1,0, false), Move(3, 2.0, 1,0,3,0, true)]

moveset = MoveSet(match_moves=match_moves, hor_moves=hor_moves, vert_moves = vert_moves)

ScoreScheme

Defines the scoring parameters used in alignment.

ScoreScheme(
    match_score::Float64,
    mismatch_score::Float64,
    extension_score::Float64,
    edge_ext_begin::Bool,
    edge_ext_end::Bool,
    kmerlength::Int
)
# default values
ScoreScheme(; match_score=0.0, mismatch_score=0.5,extension_score=0.1,edge_ext_begin=true,edge_ext_end=true,kmerlength=21)

Fields

• match_score: Score for matching bases (typically 0).
• mismatch_score: Penalty for a mismatch.
• extension_score: Penalty for extending a gap.
• edge_ext_begin: Allow gap extension from the beginning of a sequence.
• edge_ext_end: Allow gap extension from the end of a sequence.
• kmerlength: Length of kmers used in alignment seeding (if applicable).

Examples

Use the default scoring with:

scoreScheme = std_codon_scoring()

For custom scoring we can se the keyword constructor. Fields that are left out are kept at their default values.

scoreScheme = scoreScheme(match_score = 0.0, mismatch_score = 0.5, extension_score = 0.3)

LongDNA{4}

See LongDNA in the BioSequences.jl documentation.

See Also

• API Reference