sequence

Documentation

Overview

Sequence package provides a Dseq struct that represents a double stranded DNA sequence.

Index

• type Cutter
• type Dseq
  • func NewDseq(watson, crick string, overhang int, geometry constants.SequenceGeometry) *Dseq
  • func NewFromWatsonStrand(watson string, geometry constants.SequenceGeometry) *Dseq
  • func (dSeq *Dseq) Cut(enzyme Cutter) []Dseq
  • func (dSeq *Dseq) Print()

Types

type Cutter

type Cutter interface {
	GetNextRecognitionSite(sequence string, offset int, isCircular bool) []enzyme.RecognitionSiteResult
}

type Dseq

type Dseq struct {
	// A string representing the watson (sense) DNA strand.
	Watson string

	// A string representing the crick (antisense) DNA strand.
	Crick string

	// A positive or negative number to describe the stagger between
	// start of the watson and crick strands.
	Overhang int

	// A string representing the geometry of the DNA sequence. Can be "linear" or "circular".
	Geometry constants.SequenceGeometry
}

func NewDseq

func NewDseq(watson, crick string, overhang int, geometry constants.SequenceGeometry) *Dseq

func NewFromWatsonStrand

func NewFromWatsonStrand(watson string, geometry constants.SequenceGeometry) *Dseq

func (*Dseq) Cut

func (dSeq *Dseq) Cut(enzyme Cutter) []Dseq

Cut the Dseq with the provided enzyme.

Takes either a single enzyme or a batch of enzymes (RestrictionBatch).

Returns a slice of Dseqs that represent the fragments of the Dseq after cutting with the enzyme.

If the enzyme is circular, the sequence is treated as circular and the function will return the next recognition site, even if it spans the beginning and end of the sequence.

func (*Dseq) Print

func (dSeq *Dseq) Print()