Matches in SemOpenAlex for { <https://semopenalex.org/work/W2952802059> ?p ?o ?g. }
- W2952802059 endingPage "e5862" @default.
- W2952802059 startingPage "e5862" @default.
- W2952802059 abstract "We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase. σ 70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the −35 and −10 hexamer regions of σ 70 -binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the −35 and −10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the −10 and −35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts −10 and −35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service ( https://promoterpredict.com ) and standalone tool ( https://github.com/PromoterPredict ). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes." @default.
- W2952802059 created "2019-06-27" @default.
- W2952802059 creator A5046482216 @default.
- W2952802059 creator A5051715668 @default.
- W2952802059 creator A5086371599 @default.
- W2952802059 date "2018-11-07" @default.
- W2952802059 modified "2023-10-17" @default.
- W2952802059 title "PromoterPredict: sequence-based modelling of<i>Escherichia coli</i>σ<sup>70</sup>promoter strength yields logarithmic dependence between promoter strength and sequence" @default.
- W2952802059 cites W116193106 @default.
- W2952802059 cites W126745639 @default.
- W2952802059 cites W1498410508 @default.
- W2952802059 cites W1518026427 @default.
- W2952802059 cites W1594947347 @default.
- W2952802059 cites W1969395440 @default.
- W2952802059 cites W1979200451 @default.
- W2952802059 cites W1982228455 @default.
- W2952802059 cites W1992026284 @default.
- W2952802059 cites W1993154270 @default.
- W2952802059 cites W2003479120 @default.
- W2952802059 cites W2020251999 @default.
- W2952802059 cites W2041890054 @default.
- W2952802059 cites W2047360542 @default.
- W2952802059 cites W2047882868 @default.
- W2952802059 cites W2054735322 @default.
- W2952802059 cites W2071424950 @default.
- W2952802059 cites W2072361909 @default.
- W2952802059 cites W2080233018 @default.
- W2952802059 cites W2089632280 @default.
- W2952802059 cites W2111441093 @default.
- W2952802059 cites W2112264024 @default.
- W2952802059 cites W2117357746 @default.
- W2952802059 cites W2122291638 @default.
- W2952802059 cites W2126939295 @default.
- W2952802059 cites W2140952049 @default.
- W2952802059 cites W2158266834 @default.
- W2952802059 cites W2166277117 @default.
- W2952802059 cites W2168597324 @default.
- W2952802059 cites W2232370058 @default.
- W2952802059 cites W2588481196 @default.
- W2952802059 doi "https://doi.org/10.7717/peerj.5862" @default.
- W2952802059 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6228582" @default.
- W2952802059 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30425888" @default.
- W2952802059 hasPublicationYear "2018" @default.
- W2952802059 type Work @default.
- W2952802059 sameAs 2952802059 @default.
- W2952802059 citedByCount "18" @default.
- W2952802059 countsByYear W29528020592019 @default.
- W2952802059 countsByYear W29528020592020 @default.
- W2952802059 countsByYear W29528020592021 @default.
- W2952802059 countsByYear W29528020592022 @default.
- W2952802059 countsByYear W29528020592023 @default.
- W2952802059 crossrefType "journal-article" @default.
- W2952802059 hasAuthorship W2952802059A5046482216 @default.
- W2952802059 hasAuthorship W2952802059A5051715668 @default.
- W2952802059 hasAuthorship W2952802059A5086371599 @default.
- W2952802059 hasBestOaLocation W29528020591 @default.
- W2952802059 hasConcept C101762097 @default.
- W2952802059 hasConcept C104317684 @default.
- W2952802059 hasConcept C150194340 @default.
- W2952802059 hasConcept C153911025 @default.
- W2952802059 hasConcept C189754071 @default.
- W2952802059 hasConcept C2776449523 @default.
- W2952802059 hasConcept C2778112365 @default.
- W2952802059 hasConcept C33923547 @default.
- W2952802059 hasConcept C54355233 @default.
- W2952802059 hasConcept C547475151 @default.
- W2952802059 hasConcept C70721500 @default.
- W2952802059 hasConcept C86803240 @default.
- W2952802059 hasConceptScore W2952802059C101762097 @default.
- W2952802059 hasConceptScore W2952802059C104317684 @default.
- W2952802059 hasConceptScore W2952802059C150194340 @default.
- W2952802059 hasConceptScore W2952802059C153911025 @default.
- W2952802059 hasConceptScore W2952802059C189754071 @default.
- W2952802059 hasConceptScore W2952802059C2776449523 @default.
- W2952802059 hasConceptScore W2952802059C2778112365 @default.
- W2952802059 hasConceptScore W2952802059C33923547 @default.
- W2952802059 hasConceptScore W2952802059C54355233 @default.
- W2952802059 hasConceptScore W2952802059C547475151 @default.
- W2952802059 hasConceptScore W2952802059C70721500 @default.
- W2952802059 hasConceptScore W2952802059C86803240 @default.
- W2952802059 hasLocation W29528020591 @default.
- W2952802059 hasLocation W29528020592 @default.
- W2952802059 hasLocation W29528020593 @default.
- W2952802059 hasLocation W29528020594 @default.
- W2952802059 hasLocation W29528020595 @default.
- W2952802059 hasOpenAccess W2952802059 @default.
- W2952802059 hasPrimaryLocation W29528020591 @default.
- W2952802059 hasRelatedWork W1978817689 @default.
- W2952802059 hasRelatedWork W1986860360 @default.
- W2952802059 hasRelatedWork W2017988909 @default.
- W2952802059 hasRelatedWork W2032638698 @default.
- W2952802059 hasRelatedWork W2049613898 @default.
- W2952802059 hasRelatedWork W2061638026 @default.
- W2952802059 hasRelatedWork W2101976535 @default.
- W2952802059 hasRelatedWork W2114735044 @default.
- W2952802059 hasRelatedWork W2341275921 @default.
- W2952802059 hasRelatedWork W2134533779 @default.
- W2952802059 hasVolume "6" @default.