codon

Documentation

Overview

Package codon is a package for optimizing codons for expression when synthesizing DNA.

This package contains almost everything you need to do standard codon optimization.

Biological context: certain cells favor certain codons and will reject or under express sequences that don't use a similar ratio of codons. This is called codon bias: https://en.wikipedia.org/wiki/Codon_usage_bias

Furthermore, different ribosomes in different organisms will interpret codons differently. What may be a start codon for one ribosome may be a stop in the other. Heck, apparently nucleomorphs contain 4 different kinds of ribosomes. https://en.wikipedia.org/wiki/Nucleomorph <- Thanks Keoni for mentioning this example!

TTFN, Tim

Index

• func Optimize(aminoAcids string, codonTable Table, randomState ...int) (string, error)
• func Translate(sequence string, codonTable Table) (string, error)
• func WriteCodonJSON(codonTable Table, path string)
• type AminoAcid
• type Codon
• type Table
  • func AddCodonTable(firstCodonTable, secondCodonTable Table) Table
  • func CompromiseCodonTable(firstCodonTable, secondCodonTable Table, cutOff float64) (Table, error)
  • func GetCodonTable(index int) Table
  • func ParseCodonJSON(file []byte) Table
  • func ReadCodonJSON(path string) Table

Examples

• AddCodonTable
• CompromiseCodonTable
• Optimize
• ParseCodonJSON
• ReadCodonJSON
• Translate
• WriteCodonJSON

Functions

func Optimize

func Optimize(aminoAcids string, codonTable Table, randomState ...int) (string, error)

Optimize takes an amino acid sequence and codonTable and returns an optimized codon sequence. Takes an optional random seed as last argument.

Example

package main

import (
	"fmt"
	"strings"

	"github.com/TimothyStiles/poly/io/genbank"
	"github.com/TimothyStiles/poly/synthesis/codon"
)

func main() {

	gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*"

	sequence, _ := genbank.Read("../../data/puc19.gbk")
	codonTable := codon.GetCodonTable(11)

	// a string builder to build a single concatenated string of all coding regions
	var codingRegionsBuilder strings.Builder

	// iterate through the features of the genbank file and if the feature is a coding region, append the sequence to the string builder
	for _, feature := range sequence.Features {
		if feature.Type == "CDS" {
			sequence, _ := feature.GetSequence()
			codingRegionsBuilder.WriteString(sequence)
		}
	}

	// get the concatenated sequence string of the coding regions
	codingRegions := codingRegionsBuilder.String()

	// weight our codon optimization table using the regions we collected from the genbank file above
	optimizationTable := codonTable.OptimizeTable(codingRegions)

	optimizedSequence, _ := codon.Optimize(gfpTranslation, optimizationTable)
	optimizedSequenceTranslation, _ := codon.Translate(optimizedSequence, optimizationTable)

	fmt.Println(optimizedSequenceTranslation == gfpTranslation)
}

Output:

true

func Translate

func Translate(sequence string, codonTable Table) (string, error)

Translate translates a codon sequence to an amino acid sequence

Example

package main

import (
	"fmt"

	"github.com/TimothyStiles/poly/synthesis/codon"
)

func main() {

	gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*"
	gfpDnaSequence := "ATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA"
	testTranslation, _ := codon.Translate(gfpDnaSequence, codon.GetCodonTable(11)) // need to specify which codons map to which amino acids per NCBI table

	fmt.Println(gfpTranslation == testTranslation)
}

Output:

true

func WriteCodonJSON

func WriteCodonJSON(codonTable Table, path string)

WriteCodonJSON writes a codonTable struct out to JSON.

Example

package main

import (
	"fmt"
	"os"

	"github.com/TimothyStiles/poly/synthesis/codon"
)

func main() {
	codontable := codon.ReadCodonJSON("../../data/bsub_codon_test.json")
	codon.WriteCodonJSON(codontable, "../../data/codon_test.json")
	testCodonTable := codon.ReadCodonJSON("../../data/codon_test.json")

	// cleaning up test data
	os.Remove("../../data/codon_test.json")

	fmt.Println(testCodonTable.GetAminoAcids()[0].Codons[0].Weight)
}

Output:

28327

Types

type AminoAcid

type AminoAcid struct {
	Letter string  `json:"letter"`
	Codons []Codon `json:"codons"`
}

AminoAcid holds information for an amino acid and related codons in a struct

type Codon

type Codon struct {
	Triplet string `json:"triplet"`
	Weight  int    `json:"weight"` // needs to be set to 1 for random chooser
}

Codon holds information for a codon triplet in a struct

type Table

type Table interface {
	Chooser() (map[string]weightedRand.Chooser, error)
	GenerateTranslationTable() map[string]string
	GetAminoAcids() []AminoAcid
	GetStartCodons() []string
	GetStopCodons() []string
	IsEmpty() bool
	OptimizeTable(string) Table
}

Table is an interface that specifies the functions that all table types must implement

func AddCodonTable

func AddCodonTable(firstCodonTable, secondCodonTable Table) Table

AddCodonTable takes 2 CodonTables and adds them together to create a new codonTable.

Example

package main

import (
	"fmt"
	"strings"

	"github.com/TimothyStiles/poly/io/genbank"
	"github.com/TimothyStiles/poly/synthesis/codon"
)

func main() {
	sequence, _ := genbank.Read("../../data/puc19.gbk")
	codonTable := codon.GetCodonTable(11)

	// a string builder to build a single concatenated string of all coding regions
	var codingRegionsBuilder strings.Builder

	// iterate through the features of the genbank file and if the feature is a coding region, append the sequence to the string builder
	for _, feature := range sequence.Features {
		if feature.Type == "CDS" {
			sequence, _ := feature.GetSequence()
			codingRegionsBuilder.WriteString(sequence)
		}
	}

	// get the concatenated sequence string of the coding regions
	codingRegions := codingRegionsBuilder.String()

	// weight our codon optimization table using the regions we collected from the genbank file above
	optimizationTable := codonTable.OptimizeTable(codingRegions)

	sequence2, _ := genbank.Read("../../data/phix174.gb")
	codonTable2 := codon.GetCodonTable(11)

	// a string builder to build a single concatenated string of all coding regions
	var codingRegionsBuilder2 strings.Builder

	// iterate through the features of the genbank file and if the feature is a coding region, append the sequence to the string builder
	for _, feature := range sequence2.Features {
		if feature.Type == "CDS" {
			sequence, _ := feature.GetSequence()
			codingRegionsBuilder2.WriteString(sequence)
		}
	}

	// get the concatenated sequence string of the coding regions
	codingRegions2 := codingRegionsBuilder2.String()

	// weight our codon optimization table using the regions we collected from the genbank file above
	optimizationTable2 := codonTable2.OptimizeTable(codingRegions2)

	finalTable := codon.AddCodonTable(optimizationTable, optimizationTable2)
	for _, aa := range finalTable.GetAminoAcids() {
		for _, codon := range aa.Codons {
			if codon.Triplet == "GGC" {
				fmt.Println(codon.Weight)
			}
		}
	}
}

Output:

90

func CompromiseCodonTable

func CompromiseCodonTable(firstCodonTable, secondCodonTable Table, cutOff float64) (Table, error)

CompromiseCodonTable takes 2 CodonTables and makes a new codonTable that is an equal compromise between the two tables.

Example

package main

import (
	"fmt"
	"strings"

	"github.com/TimothyStiles/poly/io/genbank"
	"github.com/TimothyStiles/poly/synthesis/codon"
)

func main() {
	sequence, _ := genbank.Read("../../data/puc19.gbk")
	codonTable := codon.GetCodonTable(11)

	// a string builder to build a single concatenated string of all coding regions
	var codingRegionsBuilder strings.Builder

	// iterate through the features of the genbank file and if the feature is a coding region, append the sequence to the string builder
	for _, feature := range sequence.Features {
		if feature.Type == "CDS" {
			sequence, _ := feature.GetSequence()
			codingRegionsBuilder.WriteString(sequence)
		}
	}

	// get the concatenated sequence string of the coding regions
	codingRegions := codingRegionsBuilder.String()

	// weight our codon optimization table using the regions we collected from the genbank file above
	optimizationTable := codonTable.OptimizeTable(codingRegions)

	sequence2, _ := genbank.Read("../../data/phix174.gb")
	codonTable2 := codon.GetCodonTable(11)
	// a string builder to build a single concatenated string of all coding regions
	var codingRegionsBuilder2 strings.Builder

	// iterate through the features of the genbank file and if the feature is a coding region, append the sequence to the string builder
	for _, feature := range sequence2.Features {
		if feature.Type == "CDS" {
			sequence, _ := feature.GetSequence()
			codingRegionsBuilder2.WriteString(sequence)
		}
	}

	// get the concatenated sequence string of the coding regions
	codingRegions2 := codingRegionsBuilder2.String()

	// weight our codon optimization table using the regions we collected from the genbank file above
	optimizationTable2 := codonTable2.OptimizeTable(codingRegions2)

	finalTable, _ := codon.CompromiseCodonTable(optimizationTable, optimizationTable2, 0.1)
	for _, aa := range finalTable.GetAminoAcids() {
		for _, codon := range aa.Codons {
			if codon.Triplet == "TAA" {
				fmt.Println(codon.Weight)
			}
		}
	}
}

Output:

2727

func GetCodonTable

func GetCodonTable(index int) Table

GetCodonTable takes the index of desired NCBI codon table and returns it.

func ParseCodonJSON

func ParseCodonJSON(file []byte) Table

ParseCodonJSON parses a codonTable JSON file.

Example

package main

import (
	"fmt"
	"os"

	"github.com/TimothyStiles/poly/synthesis/codon"
)

func main() {
	file, _ := os.ReadFile("../../data/bsub_codon_test.json")
	codontable := codon.ParseCodonJSON(file)

	fmt.Println(codontable.GetAminoAcids()[0].Codons[0].Weight)
}

Output:

28327

func ReadCodonJSON

func ReadCodonJSON(path string) Table

ReadCodonJSON reads a codonTable JSON file.

Example

package main

import (
	"fmt"

	"github.com/TimothyStiles/poly/synthesis/codon"
)

func main() {
	codontable := codon.ReadCodonJSON("../../data/bsub_codon_test.json")

	fmt.Println(codontable.GetAminoAcids()[0].Codons[0].Weight)
}

Output:

28327