README
¶
RBS Calculator
For an explaination of what the RBS calculator is and how it works, please see the comments in rbs_calculator.go.
To develop a model of your own, please have a look at the comments in the model.go file in the model subpackage.
Statistics compared to the orignal Salis Lab RBS Calc v2.1
The resulting values from our model differs from the original model for the following reasons:
- We may have incorrectly understood some part of the original model (our model was developed through reading research papers and converting them to code)
- Our model uses the Linearfold version of ViennaRNA (to speed up the folding process) while the orignial model doesn't. This leads to different folding structures, and hence different free-energy values.
- To find the shine-dalgarno binding site, the original model co-folds the mRNA sequence with the 16s rRNA sequence. The resulting free-energy value includes the hybridization energy of the mRNA-rRNA binding site (the shine-dalgarno site) and the free energies of the intramolecular folding of the regions upstream and downstream of the binding site on the five prime untranslated region of the mRNA. We achieve the same value by accessing the relevant hybridization free-energy value from a lookup table (which contains the hybridization free-energy values of every possilbe mRNA-rRNA combination), and adding the free-energy values that occurs from folding the upstream and downstream regions on the mRNA sequence. We're not sure if our method gives the same results as co-folding two sequences.
Statistics from the original Salis Lab RBS Calc v2.1
| SUBGROUP | 10-fold Error | 2-fold Error | 5-fold Error | AUROC | CV | KL-divergence | Max KL-divergence | N-outliers | N-states | Normalized KL-divergence | Pearson R-squared | Pearson p | RIG | RMSE | Spearman R-squared | Spearman p | intercept | slope | Sequence entropy | MC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Kosuri_PNAS_2013 | 0.993671 | 0.736777 | 0.924164 | 0.774965 | 1.948457 | 0.979609853 | 4.60517019 | 660 | 11 | 0.212719577 | 0.279536 | 0 | 0.351527 | 1.010964 | 0.279536 | 0 | 10.25464 | -0.175 | 1209.7078 | 3742.154 |
| Goodman_Science_2013 | 0.944269 | 0.453411 | 0.711638 | 0.53305 | 2.019236 | 0.980949194 | 4.60517019 | 185 | 6 | 0.213010411 | 0.006964 | 9.81E-14 | 0.093707 | 1.610614 | 0.006964 | 9.81E-14 | 10.8653 | -0.037 | 1404.5946 | 526.4802 |
| ALL | 0.97032 | 0.602837 | 0.823708 | 0.738169 | 1.981913 | 0.900072073 | 4.60517019 | 2166 | 11 | 0.195448167 | 0.16712 | 0 | 0.221241 | 1.32865 | 0.16712 | 0 | - | - | 1447.568 | 2818.294 |
Statistics from our version of the Salis Lab RBS Calc v2.1
| SUBGROUP | 10-fold Error | 2-fold Error | 5-fold Error | AUROC | CV | KL-divergence | Max KL-divergence | N-outliers | N-states | Normalized KL-divergence | Pearson R-squared | Pearson p | RIG | RMSE | Spearman R-squared | Spearman p | intercept | invalid count | dataset size | slope |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Kosuri_PNAS_2013 | 0.992202 | 0.47344 | 0.766162 | 0.656487 | 0.979322 | 0.997283 | 4.60517 | 71 | 4 | 0.216557 | 0.0924922 | 1.04052e-188 | 0.197295 | 1.40919 | 0.0924922 | 1.04052e-188 | 10.2217 | 0 | 8848 | -0.115384 |
| Goodman_Science_2013 | 1 | 1 | 1 | 0.534554 | 1.27911 | 1.78756 | 4.60517 | 57 | 1 | 0.388163 | 0.00535533 | 6.80624e-11 | nan | 0.482264 | 0.00535533 | 6.80624e-11 | 8.17327 | 0 | 7931 | 0.00634291 |
| Kosuri_PNAS_2013 + Goodman_Science_2013 | 0.998689 | 0.592109 | 0.833065 | 0.855363 | 1.12102 | 1.10263 | 4.60517 | 283 | 4 | 0.239433 | 0.239092 | 0 | 0.267274 | 1.21933 | 0.239092 | 0 | 9.76937 | 0 | 16779 | -0.0836254 |
Statistics have been computed using the file ./model/stats.py which has been taken from the SynBioMTS with minor modifications.
Documentation
¶
Index ¶
- Constants
- Variables
- func PrintBindingSites(bindingSites []model.RibosomeBindingSite, ...)
- func RibosomeBindingSiteDefined5UTR(fivePrimeUTR, codingSequence string) (float64, error)
- func RibosomeBindingSites(ribosomalRNA, mRNA string, temperatureInCelsius float64, ...) (ribosomeBindingSites []model.RibosomeBindingSite)
- func SortByTranslationInitiationRate(ribosomeBindingSites []model.RibosomeBindingSite) []model.RibosomeBindingSite
- func TranslationInitiationRate(fivePrimeUTR, proteinCodingSequence, ribosomalRNA string, ...) (translationInitiationRate float64, ...)
- type PropertyToPrint
- type StartCodon
Examples ¶
Constants ¶
View Source
const ( AUG StartCodon = "AUG" GUG = "GUG" UUG = "UUG" CUG = "CUG" AUC = "AUC" AUA = "AUA" AUU = "AUU" CAU = "CAU" GGA = "GGA" UGC = "UGC" CGC = "CGC" UAG = "UAG" )
Variables ¶
View Source
var DefaultStartCodons []StartCodon = []StartCodon{AUG, GUG, CUG}
DefaultStartCodons are AUG, GUG and CUG
View Source
var Organism16SrRNAMap map[string]string = map[string]string{
"Bacillus subtilis subsp. subtilis str. 168": "ACCUCCUUU",
"Bacteroides thetaiotaomicron VPI-5482": "ACCUCCUUA",
"Corynebacterium glutamicum B-2784": "ACCUCCUUU",
"Escherichia coli BL21(DE3)": "ACCUCCUUA",
"Escherichia coli str. K-12 substr. DH10B": "ACCUCCUUA",
"Escherichia coli str. K-12 substr. MG1655": "ACCUCCUUA",
"Pseudomonas fluorescens A506": "ACCUCCUUA",
"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2": "ACCUCCUUA",
}
Organism16SrRNAMap is a map of an organism to its 16S ribosomal RNA.
Functions ¶
func PrintBindingSites ¶
func PrintBindingSites(bindingSites []model.RibosomeBindingSite, includeSequences, includeStructures bool, additionalPropertiesToPrint ...PropertyToPrint)
PrintBindingSites prints the important properties of a binding site. The optional argument `additionalPropertiesToPrint` specifies the computed properties of the binding site that will be printed.
func RibosomeBindingSiteDefined5UTR ¶
RibosomeBindingSiteDefined5UTREcoli37 returns a translational initiation rate of a given 5utr + protein coding sequence in E.coli at 37.
Example ¶
fivePrimeUTR := strings.ReplaceAll("GTTTATTGAAATGAACGGCTCTTTTGCTGACGAGAACAGGGGCTGGTGAA", "T", "U")
codingSequence := strings.ReplaceAll("ATGCAGTTTAAGGTTTACACCTATAAAAGAGAGAGCCGTTATCGTCTGTTTGTGGATGTACAGAGTGATATTATTGACACGCCCGGGCGACGGATGGTGATCCCCCTGGCCAGTGCACGTCTGCTGTCAGATAAAGTCTCCCGTGAACTTTACCCGGTGGTGCATATCGGGGATGAAAGCTGGCGCATGATGACCACCGATATGGCCAGTGTGCCGGTCTCCGTTATCGGGGAAGAAGTGGCTGATCTCAGCCACCGCGAAAATGACATCAAAAACGCCATTAACCTGATGTTCTGGGGAATATAA", "T", "U")
tir, _ := RibosomeBindingSiteDefined5UTR(fivePrimeUTR, codingSequence)
fmt.Println(tir)
Output: 790.3284547648203
func RibosomeBindingSites ¶
func RibosomeBindingSites(ribosomalRNA, mRNA string, temperatureInCelsius float64, startCodons []StartCodon) (ribosomeBindingSites []model.RibosomeBindingSite)
RibosomeBindingSites returns a list of ribosome binding sites for a given messenger RNA (mRNA) strand and 16s rRNA. Each site contains information about the five prime untranslated region, the protein coding sequence, the translation initiation rate as well as all the properties that were computed to figure out the translation initiation rate.
The translation initiation rates of the binding sites can be compared with each other to help you figure out where a ribosome is likely to bind to your mRNA strand.
The output can also be used to increase the amount of synthesis of your desired protein. Redesign your mRNA sequence to have higher translation initiation rates and this *should* lead to an increase in the amount of protein synthesized by your mRNA strand in-vitro.
Use the exported map `Organism16SrRNAMap` to find the 16s rRNA of the organism the mRNA strand is inserted into.
Example ¶
`cd` into this directory and run with `go test -run ^ExampleRibosomeBindingSites | less -S`. Piping to `less -S` allows you to view the complete horizontal output (use the left and right arrow keys to scroll horizontally)
startCodons := []StartCodon{AUG, GUG}
mRNA := "UCUAGAGGCCGACGCAAGCCCAUAUCGGGGCUUCCGUCGGCCAUAAGGAGGUAAAAAAUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUCAUGCGUUUCAAAGUUCGUAUGGAAGGUUCCGUUAACGGUCACGAGUUCGAAAUCGAAGGUGAAGGUGAA"
ribosomeBindingSites := RibosomeBindingSites(eColi16SrRNA, mRNA, 37.0, startCodons)
includeSequences, includeStructures := false, false
PrintBindingSites(ribosomeBindingSites, includeSequences, includeStructures)
Output: +----------------+--------------------+ | Start position | TIR | +----------------+--------------------+ | 57 | 1171.6329975491612 | +----------------+--------------------+ | 90 | 169.20068627454035 | +----------------+--------------------+ | 108 | 65.61704556715796 | +----------------+--------------------+ | 148 | 0.1347463219817721 | +----------------+--------------------+ | 154 | 2755.4116266795386 | +----------------+--------------------+
Example (WithPropertiesPrint) ¶
to run, cd into this directory and run with `go test -run ^ExampleRibosomeBindingSites_withPropertiesPrint | less -S`
startCodons := []StartCodon{AUG, GUG, UUG}
mRNA := "gctagcCACCGTCACACAGGAAAGtactagATGATTGAAAAAATTTGGAGCGGCGAAAGCCCGCATATGCGTAAAGGCGAAGAGCTGTTCACTGGTTTCGTCACTATTCTGGTGGAACTGGATGGTGATGTCAACGGTCATAAGTTTTCCGTGCGTGGCGAGGGTGAAGGTGACGCAACTAATGGTAAACTGACGCTGAAGTTCATCTGTACTACTGGTAAACTGCCGGTACCTTGGCCGACTCTGGTAACGACGCTGACTTATGGTGTTCAGTGCTTTGCTCGTTATCCGGACCACATGAAGCAGCATGACTTCTTCAAGTCCGCCATGCCGGAAGGCTATGTGCAGGAACGCACGATTTCCTTTAAGGATGACGGCACGTACAAAACGCGTGCGGAAGTGAAATTTGAAGGCGATACCCTGGTAAACCGCATTGAGCTGAAAGGCATTGACTTTAAAGAAGACGGCAATATCCTGGGCCATAAGCTGGAATACAATTTTAACAGCCACAATGTTTACATCACCGCCGATAAACAAAAAAATGGCATTAAAGCGAATTTTAAAATTCGCCACAACGTGGAGGATGGCAGCGTGCAGCTGGCTGATCACTACCAGCAAAACACTCCAATCGGTGATGGTCCTGTTCTGCTGCCAGACAATCACTATCTGAGCACGCAAAGCGTTCTGTCTAAAGATCCGAACGAGAAACGCGATCACATGGTTCTGCTGGAGTTCGTAACCGCAGCGGGCATCACGCATGGTATGGATGAACTGTACAAATAA"
ribosomeBindingSites := RibosomeBindingSites(eColi16SrRNA, mRNA, 37.0, startCodons)
// make sure that each property included here is calculated for each RBS site
// check the `PropertiesToCompute` variable (of your RBS calculator model
// subpackage) to see the properties that can be printed
propertiesToPrint := []PropertyToPrint{
{property: salis_lab_v2_1.TotalFreeEnergy, columnHeader: "dG_total"},
{property: salis_lab_v2_1.MRNARRNAHybridizationFreeEnergy, columnHeader: "dG_mRNA_rRNA"},
{property: salis_lab_v2_1.SpacingRegionFreeEnergy, columnHeader: "dG_spacing"},
{property: salis_lab_v2_1.SpacingSequenceStackingFreeEnergy, columnHeader: "dG_stacking"},
{property: salis_lab_v2_1.StandbyModuleTotalFreeEnergy, columnHeader: "dG_standby"},
{property: salis_lab_v2_1.CDSStartCodonFreeEnergy, columnHeader: "dG_start"},
{property: salis_lab_v2_1.MRNAFreeEnergy, columnHeader: "dG_mRNA"},
}
includeSequences, includeStructures := false, false
PrintBindingSites(ribosomeBindingSites, includeSequences, includeStructures, propertiesToPrint...)
Output: +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | Start position | TIR | dG_total | dG_mRNA_rRNA | dG_spacing | dG_stacking | dG_standby | dG_start | dG_mRNA | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 30 | 20183.660797413013 | -6.21205151444689 | -10.99135151444689 | 0 | 0.1693 | 0 | -2.76 | -7.37 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 34 | 1014.9135187674386 | 0.4325484855531103 | -10.99135151444689 | 1.728 | 0.5159 | 0 | 1.81 | -7.37 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 44 | 1.0931721342382053 | 15.61804848555311 | -7.8513515144468915 | 12.768 | 1.4313999999999996 | 0 | 1.81 | -7.46 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 66 | 6.859424449641934 | 11.536848809802375 | -11.581351190197623 | 0.288 | -0.039199999999999985 | 9.629399999999999 | -2.76 | -16 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 111 | 0.07529463728617104 | 21.56344859522566 | -16.891351404774344 | 7.199999999999999 | 1.1249999999999998 | 1.0898000000000003 | -0.42 | -29.46 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 121 | 55.10848337161516 | 6.906448523700085 | -23.231351476299917 | 0 | 0.2144 | 4.553400000000002 | -2.76 | -28.13 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 124 | 0.889050417475878 | 16.077348523700085 | -21.571351476299917 | 1.1520000000000001 | 0.5159 | 6.710799999999999 | -0.42 | -29.69 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 127 | 3.234578589748651 | 13.207348554694498 | -20.9913514453055 | 0 | 0.5579 | 6.710799999999999 | -2.76 | -29.69 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 150 | 0.535153656617632 | 17.205348595225658 | -22.03135140477434 | 4.032 | 1.0949 | 1.6398000000000006 | -0.42 | -32.89 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 154 | 0.020936078490524788 | 24.40774859522566 | -17.771351404774343 | 8.448 | 1.2397 | 2.7114000000000003 | -0.42 | -30.2 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 163 | 28.47924291529307 | 8.3734 | -24.57 | 0 | 0 | 4.023400000000001 | -0.42 | -29.34 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 169 | 149.8730571801419 | 4.683148561847055 | -28.901351438152943 | 0 | 0.39170000000000005 | 4.272800000000001 | -0.42 | -29.34 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 181 | 17.748369155956762 | 9.42424859999403 | -25.47135140000597 | 2.4 | -0.008800000000000002 | 7.8344000000000005 | -2.76 | -27.43 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 233 | 0.011896317688500966 | 25.66384859522566 | -19.53135140477434 | 1.525 | -0.2126 | 10.9928 | 1.81 | -31.08 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 262 | 0.019505352484515036 | 24.565048595225655 | -18.231351404774344 | 6.048 | 0.29259999999999997 | 8.9658 | -2.76 | -30.25 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 265 | 0.028048324969143876 | 23.757848595225656 | -14.921351404774343 | 9.792000000000002 | 0.6771999999999999 | 0 | -0.42 | -28.63 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 272 | 0.7332332868074979 | 16.505548595225655 | -15.721351404774344 | 0 | 0.38449999999999995 | 3.7224000000000004 | -0.42 | -28.54 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 277 | 0.08347514428339604 | 21.33424859522566 | -17.58135140477434 | 2.4 | 0.6819999999999999 | 5.2336 | 1.81 | -28.79 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 297 | 6.807299573773182 | 11.553800000000006 | -22.549999999999997 | 0 | 0 | 5.4938 | -2.76 | -31.37 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 307 | 4.745769777928437 | 12.35544856661543 | -23.59135143338457 | 3.168 | -0.05480000000000003 | 1.5335999999999999 | -2.76 | -34.06 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 327 | 81.7385307386559 | 6.030400000000004 | -27.48 | 0 | 0 | 4.4304000000000014 | -2.76 | -31.84 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 340 | 0.2783539599919396 | 18.657927202110585 | -29.30135119019762 | 9.628878392308204 | 0 | 9.400400000000001 | -2.76 | -31.69 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 342 | 0.6923089432471177 | 16.633174391943214 | -30.461351190197625 | 0.005325582140839866 | 0.2564 | 10.8228 | -0.42 | -36.43 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 370 | 0.035882830606947205 | 23.2104485713838 | -21.611351428616203 | 9.792000000000002 | 1.0899999999999996 | 6.0098 | -2.76 | -30.69 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 391 | 0.11374100632067038 | 20.646748428332646 | -23.021351571667353 | 9.792000000000002 | -0.003699999999999995 | 5.7598 | -0.42 | -28.54 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 399 | 51.179829695166795 | 7.070799999999995 | -26.01 | 0 | 0 | 5.800799999999999 | -0.42 | -27.7 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 406 | 8.302516317178513 | 11.112548585688916 | -26.941351414311086 | 0 | 0.2635 | 8.450400000000002 | 1.81 | -27.53 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 433 | 2.184645636511025 | 14.079448595225658 | -19.141351404774344 | 1.1520000000000001 | -0.2898 | 5.458600000000002 | 1.81 | -25.09 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 448 | 0.9667632578121175 | 15.891126973228744 | -19.48135141907946 | 9.628878392308204 | 0 | 1.5335999999999999 | 1.81 | -22.4 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 511 | 0.011230450988054098 | 25.79184856661543 | -17.101351433384572 | 9.792000000000002 | 0.8257999999999998 | 16.0354 | -2.76 | -19 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 541 | 283.25158712554213 | 3.2686000000000046 | -9.72 | 0 | 0 | 0.07860000000000511 | -2.76 | -15.67 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 576 | 0.0377546603426956 | 23.09744858062252 | -12.981351419377482 | 9.792000000000002 | 1.1663999999999992 | 2.650400000000001 | -0.42 | -22.89 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 583 | 205.0277843071038 | 3.986800000000006 | -17.98 | 0 | 0 | 0.21680000000000277 | -2.76 | -24.51 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 591 | 88.50540964500519 | 5.8536485046265945 | -20.101351495373407 | 0.6719999999999999 | 0.17919999999999997 | 2.0538000000000007 | -0.42 | -23.47 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 631 | 2.1817460643419238 | 14.0824 | -19.52 | 0 | 0 | 3.7224000000000004 | -0.42 | -30.3 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 634 | 24.697585928272055 | 8.690000000000001 | -21.85 | 0 | 0 | 3 | -2.76 | -30.3 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 717 | 287.9035427873015 | 3.2324000000000055 | -23.65 | 0 | 0 | 0.7224000000000004 | -2.76 | -28.92 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 757 | 34.70499560949332 | 7.934048579728449 | -19.691351420271552 | 0.6719999999999999 | -0.099 | 5.9024 | -2.76 | -23.91 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 762 | 5.121916279058144 | 12.18594857972845 | -17.91135142027155 | 4.032 | 0.27490000000000003 | 6.420400000000001 | -2.76 | -22.13 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+ | 766 | 164.4953205580303 | 4.4762741773664985 | -20.971351404774342 | 0.005325582140839866 | 0.3015 | 5.800799999999999 | -2.76 | -22.1 | +----------------+----------------------+--------------------+---------------------+----------------------+-----------------------+---------------------+----------+---------+
Example (WithSequences) ¶
startCodons := []StartCodon{AUG, GUG}
mRNA := "UCUAGAGGCCGACGCAAGCCCAUAUCGGGGCUUCCGUCGGCCAUAAGGAGGUAAAAAAUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUCAUGCGUUUCAAAGUUCGUAUGGAAGGUUCCGUUAACGGUCACGAGUUCGAAAUCGAAGGUGAAGGUGAA"
ribosomeBindingSites := RibosomeBindingSites(eColi16SrRNA, mRNA, 37.0, startCodons)
includeSequences, includeStructures := true, false
PrintBindingSites(ribosomeBindingSites, includeSequences, includeStructures)
Output: +----------------+--------------------+------------------------------------------------------------------------------------------------------+-------------------------------------+ | Start position | TIR | 5' Untranslated Region | Protein Coding Sequence | +----------------+--------------------+------------------------------------------------------------------------------------------------------+-------------------------------------+ | 57 | 1171.6329975491612 | UCUAGAGGCCGACGCAAGCCCAUAUCGGGGCUUCCGUCGGCCAUAAGGAGGUAAAAA | AUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUCAU | +----------------+--------------------+------------------------------------------------------------------------------------------------------+-------------------------------------+ | 90 | 169.20068627454035 | UCUAGAGGCCGACGCAAGCCCAUAUCGGGGCUUCCGUCGGCCAUAAGGAGGUAAAAAAUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUC | AUGCGUUUCAAAGUUCGUAUGGAAGGUUCCGUUAA | +----------------+--------------------+------------------------------------------------------------------------------------------------------+-------------------------------------+ | 108 | 65.61704556715796 | CCGACGCAAGCCCAUAUCGGGGCUUCCGUCGGCCAUAAGGAGGUAAAAAAUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUCAUGCGUUUCAAAGUUCGU | AUGGAAGGUUCCGUUAACGGUCACGAGUUCGAAAU | +----------------+--------------------+------------------------------------------------------------------------------------------------------+-------------------------------------+ | 148 | 0.1347463219817721 | AGGUAAAAAAUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUCAUGCGUUUCAAAGUUCGUAUGGAAGGUUCCGUUAACGGUCACGAGUUCGAAAUCGAAG | GUGAAGGUGAA | +----------------+--------------------+------------------------------------------------------------------------------------------------------+-------------------------------------+ | 154 | 2755.4116266795386 | AAAAUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUCAUGCGUUUCAAAGUUCGUAUGGAAGGUUCCGUUAACGGUCACGAGUUCGAAAUCGAAGGUGAAG | GUGAA | +----------------+--------------------+------------------------------------------------------------------------------------------------------+-------------------------------------+
Example (WithStructures) ¶
startCodons := []StartCodon{AUG, GUG}
mRNA := "UCUAGAGGCCGACGCAAGCCCAUAUCGGGGCUUCCGUCGGCCAUAAGGAGGUAAAAAAUGGCGAGCUCUGAAGACGUUAUCAAAGAGUUCAUGCGUUUCAAAGUUCGUAUGGAAGGUUCCGUUAACGGUCACGAGUUCGAAAUCGAAGGUGAAGGUGAA"
ribosomeBindingSites := RibosomeBindingSites(eColi16SrRNA, mRNA, 37.0, startCodons)
includeSequences, includeStructures := false, true
PrintBindingSites(ribosomeBindingSites, includeSequences, includeStructures)
Output: +----------------+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------+--------------------------------+-----------------------+--------------------------------+-----------------------------+--------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------+ | Start position | TIR | Initial state | Final state (pre ribosome) | Final state (mRNA shine | Final state (spacing) | Final state (ribosome | Final state (post ribosome) | Final state (16S rRNA shine | Full final state | | | | | | dalgarno binding site) | | footprint) | | dalgarno binding site) | | +----------------+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------+--------------------------------+-----------------------+--------------------------------+-----------------------------+--------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------+ | 57 | 1171.6329975491612 | (((...((((((((.((((((......)))))).))))))))...)))..............(((((((...((.....))..))))))).. | ......((((((((.((((((......)))))).)))))))). | .((((((((( | ......... | ............. | ...................... | &))))))))) | ......((((((((.((((((......)))))).))))))))..(((((((((............................................&))))))))) | +----------------+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------+--------------------------------+-----------------------+--------------------------------+-----------------------------+--------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------+ | 90 | 169.20068627454035 | (((...((((((((.((((((......)))))).))))))))...)))............(((((((.((((.((((...............)))))))).)))))))(((((....)))))... | (((...((((((((.((((((......)))))).))))))))...)))..............(((((((...((.....))..))))))) | | | ............. | .....(((((....)))))... | | (((...((((((((.((((((......)))))).))))))))...)))..............(((((((...((.....))..)))))))..................(((((....)))))... | +----------------+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------+--------------------------------+-----------------------+--------------------------------+-----------------------------+--------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------+ | 108 | 65.61704556715796 | ((((((.((((((......)))))).)))))).................((..((((((((((...(((((.(......((((((((..........)))))))).......).))))).))).)))))))..)) | ((((((.((((((......)))))).))))))....................(((((((.((((.((((...............)))))))).))))))) | | | ............. | ...................... | | 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func SortByTranslationInitiationRate ¶
func SortByTranslationInitiationRate(ribosomeBindingSites []model.RibosomeBindingSite) []model.RibosomeBindingSite
SortByTranslationInitiationRate sorts a list of binding sites by their translation initiation rates in descending order
func TranslationInitiationRate ¶
func TranslationInitiationRate(fivePrimeUTR, proteinCodingSequence, ribosomalRNA string, temperateureInCelsius float64) (translationInitiationRate float64, bindingSiteWithProperties model.RibosomeBindingSite)
TranslationInitiationRate returns the the translation initiation rate of a ribsome binding site as well as the binding site (as a `model.RibosomeBindingSite` struct) with the properties computed to calculate the translation initiation rate
Types ¶
type PropertyToPrint ¶
type PropertyToPrint struct {
// contains filtered or unexported fields
}
PropertyToPrint specifies the computed property of a ribosome binding site that will be printed when using the `PrintBindingSites` func
type StartCodon ¶
type StartCodon string
StartCodon specifies the start codon of the protein coding sequence of a mRNA strand.
Source Files
Directories
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| Path | Synopsis |
|---|---|
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Package secondary_structure provides the structs needed to contain information about a RNA's secondary structure
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Package secondary_structure provides the structs needed to contain information about a RNA's secondary structure |
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