rbs_calculator

Documentation

Index

• Variables
• func LookupTable() (map[string]map[string]float64, error)
• type BindingSite
  • func RibosomeBindingSiteV1(rRNA, mRNA string) (*BindingSite, error)
  • func RibosomeBindingSiteV2(rRNA, mRNA string) (*BindingSite, error)

Examples

• LookupTable

Variables

var EColiRNA = "ACCTCCTTA"

var SalisRNA = "ATTCCTCCA"

Functions

func LookupTable

func LookupTable() (map[string]map[string]float64, error)

Example

dG_rRNA_mRNA, err := LookupTable()
if err != nil {
	fmt.Printf("Failed to initialize lookup table: %s", err)
	return
}
fmt.Println(dG_rRNA_mRNA["ACCTCCTTA"]["CAAGGAGGGTG"])

Output:

-11.9

Types

type BindingSite

type BindingSite struct {
	TranslationInitiationRate, MinimumFreeEnergy float64
	FivePrimeIdx, ThreePrimeIdx                  int
	RRNA, MRNA, MRNAStructure                    string
	MRNAFreeEnergy, MRNARRNAFreeEnergy           float64
	FoundBindingSite                             bool
}

func RibosomeBindingSiteV1

func RibosomeBindingSiteV1(rRNA, mRNA string) (*BindingSite, error)

RBS calculations according to Keoni's ideas

func RibosomeBindingSiteV2

func RibosomeBindingSiteV2(rRNA, mRNA string) (*BindingSite, error)

RBS calculations that calculates dG_mRNA_rRNA by co-folding the mRNA and rRNA sequences