fix

Documentation

Overview

Package fix fixes synthetic DNA molecules in preparation for synthesis.

Many synthesis companies have restrictions on the DNA they can synthesize. This synthesis fixer takes advantage of synonymous codons in protein coding sequences (CDS) to remove problematic sequences that either users don't want (like restriction enzymes sites) or that would cause DNA synthesis companies to reject a synthesis project.

This synthesis fixer is meant to cover the majority of use cases for DNA fixing. It is not intended to cover all possible use cases, since the majority of DNA design does not actually have these edge cases.

For most users, using `CdsSimple` will be sufficient to prepare a sequence for synthesis (you may want to add in restriction enzyme sites to remove).

Cds does not guarantee that all requested features will be removed. If you have use case that Cds cannot properly fix, please put an issue in the poly github.

Example (Basic)

This example shows basic usage of the synthesis package. In this example, we will remove BsaI sites from the bla gene, commonly found in pUC plasmids.

package main

import (
	"fmt"

	"github.com/bebop/poly/synthesis/codon"
	"github.com/bebop/poly/synthesis/fix"
)

func main() {
	// Initialize a gene. We will be using bla, or ampicillin resistance.
	bla := "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"

	// Here, we initialize a codon table. This table is used to pick the
	// appropriate new synonymous codons.
	codonTable := codon.ReadCodonJSON("../../data/pichiaTable.json")

	// Finally, we fix the sequence with the optimization table, getting
	// rid of the BsaI cut site, GGTCTC
	fixedSeq, _, _ := fix.CdsSimple(bla, codonTable, []string{"GGTCTC"})

	fmt.Println(fixedSeq)
}

Output:

ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA

Index

• func GcContentFixer(upperBound, lowerBound float64) func(string, chan DnaSuggestion, *sync.WaitGroup)
• func RemoveRepeat(repeatLen int) func(string, chan DnaSuggestion, *sync.WaitGroup)
• func RemoveSequence(sequencesToRemove []string, reason string) func(string, chan DnaSuggestion, *sync.WaitGroup)
• type Change
  • func Cds(sequence string, codontable codon.Table, ...) (string, []Change, error)
  • func CdsSimple(sequence string, codontable codon.Table, sequencesToRemove []string) (string, []Change, error)
• type DnaSuggestion

Examples

• Package (Basic)
• Cds
• CdsSimple

Functions

func GcContentFixer

func GcContentFixer(upperBound, lowerBound float64) func(string, chan DnaSuggestion, *sync.WaitGroup)

GcContentFixer is a generator to increase or decrease the overall GcContent of a CDS. GcContent is defined as the percentage of guanine and cytosine base pairs in comparison to adenine and thymine base pairs. Usually, you want the range to be somewhere around 50%, with a decent upperBound being 80% GC and a decent lowerBound being 20%.

func RemoveRepeat

func RemoveRepeat(repeatLen int) func(string, chan DnaSuggestion, *sync.WaitGroup)

RemoveRepeat is a generator to make a problematicSequenceFunc for repeats.

func RemoveSequence

func RemoveSequence(sequencesToRemove []string, reason string) func(string, chan DnaSuggestion, *sync.WaitGroup)

RemoveSequence is a generator for a problematicSequenceFuncs for specific sequences.

Types

type Change

type Change struct {
	Position int    `db:"position"`
	Step     int    `db:"step"`
	From     string `db:"codonfrom"`
	To       string `db:"codonto"`
	Reason   string `db:"reason"`
}

Change is a change to a given DNA sequence. A list of changes is given as the output of Cds.

func Cds

func Cds(sequence string, codontable codon.Table, problematicSequenceFuncs []func(string, chan DnaSuggestion, *sync.WaitGroup)) (string, []Change, error)

Cds fixes a CDS given the CDS sequence, a codon table, a list of functions to solve for, and a number of iterations to attempt fixing. Unless you are an advanced user, you should use CdsSimple.

Example

package main

import (
	"fmt"
	"sync"

	"github.com/bebop/poly/synthesis/codon"
	"github.com/bebop/poly/synthesis/fix"
)

var dataDir string = "../../data/"

func main() {
	bla := "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATACGGAAATGTTGAATACTCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"

	codonTable := codon.ReadCodonJSON(dataDir + "pichiaTable.json")

	fixedSeq, changes, _ := fix.Cds(bla, codonTable, []func(string, chan fix.DnaSuggestion, *sync.WaitGroup){fix.RemoveRepeat(20), fix.RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site")})
	fmt.Printf("Changed position %d from %s to %s for reason: %s. Complete sequence: %s", changes[1].Position, changes[1].From, changes[1].To, changes[1].Reason, fixedSeq)

}

Output:

Changed position 245 from GGG to GGA for reason: TypeIIS restriction enzyme site. Complete sequence: ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATATGGAAATGTTGAATACTCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA

func CdsSimple

func CdsSimple(sequence string, codontable codon.Table, sequencesToRemove []string) (string, []Change, error)

CdsSimple is FixCds with some defaults for normal usage, including removing of homopolymers, removing any repeat larger than 18 base pairs, and fixing if a CDS's gc content is above 80% or below 20%

Example

package main

import (
	"fmt"

	"github.com/bebop/poly/synthesis/codon"
	"github.com/bebop/poly/synthesis/fix"
)

var dataDir string = "../../data/"

func main() {
	bla := "ATGAAAAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"

	codonTable := codon.ReadCodonJSON(dataDir + "pichiaTable.json")

	fixedSeq, changes, _ := fix.CdsSimple(bla, codonTable, []string{"GGTCTC"})
	fmt.Printf("Changed position %d from %s to %s for reason: %s. Complete sequence: %s", changes[0].Position, changes[0].From, changes[0].To, changes[0].Reason, fixedSeq)

}

Output:

Changed position 1 from AAA to AAG for reason: Homopolymers. Complete sequence: ATGAAGAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA

type DnaSuggestion

type DnaSuggestion struct {
	Start          int    `db:"start"`
	End            int    `db:"end"`
	Bias           string `db:"gcbias"`
	QuantityFixes  int    `db:"quantityfixes"`
	SuggestionType string `db:"suggestiontype"`
}

DnaSuggestion is a suggestion of a fixer, generated by a problematicSequenceFunc. Bias must be `NA`, `GC`, or `AT`, with `NA` representing a neutral skew.