clone

Documentation

Overview

Package clone provides functions for cloning DNA sequences.

Since 1973, the most common way to make recombinant DNA has been restriction enzyme cloning (though lately, homologous recombination based methods like Gibson assembly have attracted a lot of use). The cloning functions here allow for simulation of restriction enzyme cloning.

For a historical review leading up to the discovery: https://doi.org/10.1073/pnas.1313397110

The idea of restriction enzyme cloning is that you can cut DNA at specific locations with restriction enzyme and then glue them back together in different patterns using ligase. The final product is (99.9% of the time) a circular plasmid that you can transform into a bacterial cell for propagation.

While simulation is simple for simple cases, there are a lot of edge cases to handle, for example:

• Which input sequences are circular? How do we handle their rotations?
• Is the enzyme that is cutting directional? How do we handle that directionality?
• Are there multiple possible outputs of our ligation reaction? For example, ligations may be able to create a "library" of plasmids, in which there are millions of valid combinations.
• How do we handle sequences that get ligated in multiple orientations?

These cloning functions handle all those problems so that they appear simple to the end user.

In particular, there is a focus here on GoldenGate Assembly: https://en.wikipedia.org/wiki/Golden_Gate_Cloning https://www.neb.com/applications/cloning-and-synthetic-biology/dna-assembly-and-cloning/golden-gate-assembly

GoldenGate is a particular kind of restriction enzyme cloning reaction that you can do in a single tube and that is extraordinarily efficient (up to 50 parts) and is popular for new modular DNA part toolkits. Users can easily simulate GoldenGate assembly reactions with just their input fragments + the enzyme name.

Unlike many other GoldenGate simulators, we support simulating GoldenGate with methylated DNA sequences, which are represented as lowercased sequences in user inputted sequences. Normally, this can be turned off, but can be used in the special case of recursive GoldenGate reactions.

Let's build some DNA!

Keoni

PS: We do NOT (yet) handle restriction enzymes which recognize one site but cut in multiple places (Type IIG enzymes) such as BcgI.

Index

• Variables
• func GoldenGate(sequences []Part, cuttingEnzyme Enzyme, methylated bool) (string, []int, error)
• func Ligate(fragments []Fragment, circular bool) (string, []int, error)
• type Enzyme
• type Fragment
  • func CutWithEnzyme(part Part, directional bool, enzyme Enzyme, methylated bool) []Fragment
  • func CutWithEnzymeByName(part Part, directional bool, name string, methylated bool) ([]Fragment, error)
• type KmerOverlap
  • func FindKmerOverlaps(fragments []Fragment, ligationProduct string, ligationPattern []int, ...) ([]KmerOverlap, error)
  • func FindKmers(kmerOverlaps []KmerOverlap, read fastq.Read) []KmerOverlap
• type Overhang
• type Part

Examples

• GoldenGate

Variables

var DefaultEnzymes = map[string]Enzyme{
	"BsaI":  {"BsaI", regexp.MustCompile("GGTCTC"), regexp.MustCompile("GAGACC"), 1, 4, "GGTCTC"},
	"BbsI":  {"BbsI", regexp.MustCompile("GAAGAC"), regexp.MustCompile("GTCTTC"), 2, 4, "GAAGAC"},
	"BtgZI": {"BtgZI", regexp.MustCompile("GCGATG"), regexp.MustCompile("CATCGC"), 10, 4, "GCGATG"},
	"PaqCI": {"PaqCI", regexp.MustCompile("CACCTGC"), regexp.MustCompile("GCAGGTG"), 4, 4, "CACCTGC"},
	"BsmBI": {"BsmBI", regexp.MustCompile("CGTCTC"), regexp.MustCompile("GAGACG"), 1, 4, "CGTCTC"},
}

Functions

func GoldenGate

func GoldenGate(sequences []Part, cuttingEnzyme Enzyme, methylated bool) (string, []int, error)

GoldenGate simulates a GoldenGate cloning reaction. As of right now, we only support BsaI, BbsI, BtgZI, and BsmBI. Set methylated flag to true if there is lowercase methylated DNA as part of the sequence.

Example

package main

import (
	"fmt"
	"log"

	"github.com/koeng101/dnadesign/lib/clone"
)

func main() {
	// Fragment 1 has a palindrome at its start. This isn't very common but
	// can occur. These two fragments are real DNA fragments used in the
	// FreeGenes Project. They are used because they were on my computer
	// - Keoni
	fragment1 := clone.Part{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false}
	fragment2 := clone.Part{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false}

	// pOpen plasmid series (https://stanford.freegenes.org/collections/open-genes/products/open-plasmids#description). I use it for essentially all my cloning. -Keoni
	var popen = clone.Part{"TAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGGCCTACTATTAGCAACAACGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACCTGCACCAGTCAGTAAAACGACGGCCAGTAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTTGGTTCAGGTGGAGTGGGAGTAgtcttcGCcatcgCtACTAAAagccagataacagtatgcgtatttgcgcgctgatttttgcggtataagaatatatactgatatgtatacccgaagtatgtcaaaaagaggtatgctatgaagcagcgtattacagtgacagttgacagcgacagctatcagttgctcaaggcatatatgatgtcaatatctccggtctggtaagcacaaccatgcagaatgaagcccgtcgtctgcgtgccgaacgctggaaagcggaaaatcaggaagggatggctgaggtcgcccggtttattgaaatgaacggctcttttgctgacgagaacagggGCTGGTGAAATGCAGTTTAAGGTTTACACCTATAAAAGAGAGAGCCGTTATCGTCTGTTTGTGGATGTACAGAGTGATATTATTGACACGCCCGGGCGACGGATGGTGATCCCCCTGGCCAGTGCACGTCTGCTGTCAGATAAAGTCTCCCGTGAACTTTACCCGGTGGTGCATATCGGGGATGAAAGCTGGCGCATGATGACCACCGATATGGCCAGTGTGCCGGTCTCCGTTATCGGGGAAGAAGTGGCTGATCTCAGCCACCGCGAAAATGACATCAAAAACGCCATTAACCTGATGTTCTGGGGAATATAAATGTCAGGCTCCCTTATACACAGgcgatgttgaagaccaCGCTGAGGTGTCAATCGTCGGAGCCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCATGGTCATAGCTGTTTCCTGAGAGCTTGGCAGGTGATGACACACATTAACAAATTTCGTGAGGAGTCTCCAGAAGAATGCCATTAATTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGG", true}

	plasmid, _, err := clone.GoldenGate([]clone.Part{fragment1, fragment2, popen}, clone.DefaultEnzymes["BbsI"], false)
	if err != nil {
		log.Fatalf("Failed to GoldenGate. Got error: %s", err)
	}

	fmt.Println(plasmid)
}

Output:

GGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGAGGTGTCAATCGTCGGAGCCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCATGGTCATAGCTGTTTCCTGAGAGCTTGGCAGGTGATGACACACATTAACAAATTTCGTGAGGAGTCTCCAGAAGAATGCCATTAATTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGGCCTACTATTAGCAACAACGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACCTGCACCAGTCAGTAAAACGACGGCCAGTAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTTGGTTCAGGTGGAGTG

func Ligate

func Ligate(fragments []Fragment, circular bool) (string, []int, error)

Ligate simulates ligations. It assumes that fragments can only be ligated in a single way (no 2 fragments with the same overhangs), and also assumes the first fragment WILL be used in the ligation reaction. This function is a massive simplification of the original ligation code which can do more. If this does not fulfill your needs, please leave an issue in git.

Types

type Enzyme

type Enzyme struct {
	Name            string
	RegexpFor       *regexp.Regexp
	RegexpRev       *regexp.Regexp
	Skip            int
	OverheadLength  int
	RecognitionSite string
}

Enzyme is a struct that represents restriction enzymes.

type Fragment

type Fragment struct {
	Sequence        string
	ForwardOverhang string
	ReverseOverhang string
}

Fragment is a struct that represents linear DNA sequences with sticky ends.

func CutWithEnzyme

func CutWithEnzyme(part Part, directional bool, enzyme Enzyme, methylated bool) []Fragment

CutWithEnzyme cuts a given sequence with an enzyme represented by an Enzyme struct. If there is methylated parts of the target DNA, set the "methylated" flag to true and lowercase ONLY methylated DNA.

func CutWithEnzymeByName

func CutWithEnzymeByName(part Part, directional bool, name string, methylated bool) ([]Fragment, error)

CutWithEnzymeByName cuts a given sequence with an enzyme represented by the enzyme's name. It is a convenience wrapper around CutWithEnzyme that allows us to specify the enzyme by name. Set methylated flag to true if there is lowercase methylated DNA as part of the sequence.

type KmerOverlap

type KmerOverlap struct {
	Kmer      string
	Fragment1 Fragment
	Fragment2 Fragment
}

KmerOverlap represents the overlap between two fragments indicative of a ligation event.

func FindKmerOverlaps

func FindKmerOverlaps(fragments []Fragment, ligationProduct string, ligationPattern []int, kmerSize int) ([]KmerOverlap, error)

FindKmerOverlaps finds kmerOverlaps from ligation reactions. It can be used with FindKmers to find ligation events in sequence data.

Here is the problem: You have sequenced a GoldenGate or ligation you've run to assemble some DNA. How do you quantify the efficiency of the ligation from this raw data? You may want to do this to make sure your ligations are working properly in a way that simple controls wouldn't: you can *directly* observe single molecules of interest that are ligated and ones which aren't.

How would you do this? The simplest version, which we implement here, is to check whether or not kmers indicative of ligation exist within the sequenced fragments. This is simple and computationally inexpensive.

func FindKmers

func FindKmers(kmerOverlaps []KmerOverlap, read fastq.Read) []KmerOverlap

FindKmers finds kmers indicative of ligation events within fastq sequencing reads. If you need to just search raw sequence and not fastq reads, you can simply fake a fastq: we only use sequence data from it in this function.

type Overhang

type Overhang struct {
	Length                        int
	Position                      int
	Forward                       bool
	RecognitionSitePlusSkipLength int
}

Overhang is a struct that represents the ends of a linearized sequence where Enzymes had cut.

type Part

type Part struct {
	Sequence string
	Circular bool
}

Part is a simple struct that can carry a circular or linear DNA sequence. In the field of synthetic biology, the term "DNA Part" was popularized by the iGEM competition http://parts.igem.org/Main_Page , so we use that term here.