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hidden markov model using vbfret or ebfret matlab software packages  (MathWorks Inc)


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    MathWorks Inc hidden markov model using vbfret or ebfret matlab software packages
    A LSP DNA labeled with a donor/acceptor dye pair for single-molecule <t>FRET</t> <t>(smFRET)</t> assay. B Schematic of smFRET assay to study real-time, single-molecule DNA bending dynamics of TFAM. C , D , G A sample smFRET time trace (left) and FRET histogram (right) for LSP DNA alone (N Trace = 288), LSP + TFAM (N Trace = 420), and LSP + TFAM C-tail mutant (ΔCT) (N Trace = 219), respectively. E FRET transition density plot (TDP) for LSP + TFAM, showing two-state kinetics. F Dwell time histograms of the low FRET state, i.e., P-state (left), and the high FRET state, i.e., F-state (right). Red curves indicate the fitted single- and double-exponential models for P- and F-state, respectively. H Ensemble FRET spectra, showing TFAM-induced DNA bending at the ensemble level in solution. I Diagram summarizes the two-state DNA bending kinetics of the LSP-TFAM complex. The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using <t>vbFRET</t> or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.
    Hidden Markov Model Using Vbfret Or Ebfret Matlab Software Packages, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hidden markov model using vbfret or ebfret matlab software packages/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    hidden markov model using vbfret or ebfret matlab software packages - by Bioz Stars, 2026-04
    90/100 stars

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    1) Product Images from "Sequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation"

    Article Title: Sequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation

    Journal: Nature Communications

    doi: 10.1038/s41467-024-49728-6

    A LSP DNA labeled with a donor/acceptor dye pair for single-molecule FRET (smFRET) assay. B Schematic of smFRET assay to study real-time, single-molecule DNA bending dynamics of TFAM. C , D , G A sample smFRET time trace (left) and FRET histogram (right) for LSP DNA alone (N Trace = 288), LSP + TFAM (N Trace = 420), and LSP + TFAM C-tail mutant (ΔCT) (N Trace = 219), respectively. E FRET transition density plot (TDP) for LSP + TFAM, showing two-state kinetics. F Dwell time histograms of the low FRET state, i.e., P-state (left), and the high FRET state, i.e., F-state (right). Red curves indicate the fitted single- and double-exponential models for P- and F-state, respectively. H Ensemble FRET spectra, showing TFAM-induced DNA bending at the ensemble level in solution. I Diagram summarizes the two-state DNA bending kinetics of the LSP-TFAM complex. The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using vbFRET or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.
    Figure Legend Snippet: A LSP DNA labeled with a donor/acceptor dye pair for single-molecule FRET (smFRET) assay. B Schematic of smFRET assay to study real-time, single-molecule DNA bending dynamics of TFAM. C , D , G A sample smFRET time trace (left) and FRET histogram (right) for LSP DNA alone (N Trace = 288), LSP + TFAM (N Trace = 420), and LSP + TFAM C-tail mutant (ΔCT) (N Trace = 219), respectively. E FRET transition density plot (TDP) for LSP + TFAM, showing two-state kinetics. F Dwell time histograms of the low FRET state, i.e., P-state (left), and the high FRET state, i.e., F-state (right). Red curves indicate the fitted single- and double-exponential models for P- and F-state, respectively. H Ensemble FRET spectra, showing TFAM-induced DNA bending at the ensemble level in solution. I Diagram summarizes the two-state DNA bending kinetics of the LSP-TFAM complex. The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using vbFRET or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.

    Techniques Used: Labeling, Smfret Assay, Mutagenesis, Software



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    hidden markov model using vbfret or ebfret matlab software packages  (MathWorks Inc)
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    MathWorks Inc hidden markov model using vbfret or ebfret matlab software packages
    A LSP DNA labeled with a donor/acceptor dye pair for single-molecule <t>FRET</t> <t>(smFRET)</t> assay. B Schematic of smFRET assay to study real-time, single-molecule DNA bending dynamics of TFAM. C , D , G A sample smFRET time trace (left) and FRET histogram (right) for LSP DNA alone (N Trace = 288), LSP + TFAM (N Trace = 420), and LSP + TFAM C-tail mutant (ΔCT) (N Trace = 219), respectively. E FRET transition density plot (TDP) for LSP + TFAM, showing two-state kinetics. F Dwell time histograms of the low FRET state, i.e., P-state (left), and the high FRET state, i.e., F-state (right). Red curves indicate the fitted single- and double-exponential models for P- and F-state, respectively. H Ensemble FRET spectra, showing TFAM-induced DNA bending at the ensemble level in solution. I Diagram summarizes the two-state DNA bending kinetics of the LSP-TFAM complex. The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using <t>vbFRET</t> or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.
    Hidden Markov Model Using Vbfret Or Ebfret Matlab Software Packages, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hidden markov model using vbfret or ebfret matlab software packages/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    hidden markov model using vbfret or ebfret matlab software packages - by Bioz Stars, 2026-04
    90/100 stars
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    ebfret matlab software package  (MathWorks Inc)
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    MathWorks Inc ebfret matlab software package
    A LSP DNA labeled with a donor/acceptor dye pair for single-molecule <t>FRET</t> <t>(smFRET)</t> assay. B Schematic of smFRET assay to study real-time, single-molecule DNA bending dynamics of TFAM. C , D , G A sample smFRET time trace (left) and FRET histogram (right) for LSP DNA alone (N Trace = 288), LSP + TFAM (N Trace = 420), and LSP + TFAM C-tail mutant (ΔCT) (N Trace = 219), respectively. E FRET transition density plot (TDP) for LSP + TFAM, showing two-state kinetics. F Dwell time histograms of the low FRET state, i.e., P-state (left), and the high FRET state, i.e., F-state (right). Red curves indicate the fitted single- and double-exponential models for P- and F-state, respectively. H Ensemble FRET spectra, showing TFAM-induced DNA bending at the ensemble level in solution. I Diagram summarizes the two-state DNA bending kinetics of the LSP-TFAM complex. The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using <t>vbFRET</t> or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.
    Ebfret Matlab Software Package, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ebfret matlab software package/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    ebfret matlab software package - by Bioz Stars, 2026-04
    90/100 stars
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    Image Search Results


    A LSP DNA labeled with a donor/acceptor dye pair for single-molecule FRET (smFRET) assay. B Schematic of smFRET assay to study real-time, single-molecule DNA bending dynamics of TFAM. C , D , G A sample smFRET time trace (left) and FRET histogram (right) for LSP DNA alone (N Trace = 288), LSP + TFAM (N Trace = 420), and LSP + TFAM C-tail mutant (ΔCT) (N Trace = 219), respectively. E FRET transition density plot (TDP) for LSP + TFAM, showing two-state kinetics. F Dwell time histograms of the low FRET state, i.e., P-state (left), and the high FRET state, i.e., F-state (right). Red curves indicate the fitted single- and double-exponential models for P- and F-state, respectively. H Ensemble FRET spectra, showing TFAM-induced DNA bending at the ensemble level in solution. I Diagram summarizes the two-state DNA bending kinetics of the LSP-TFAM complex. The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using vbFRET or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.

    Journal: Nature Communications

    Article Title: Sequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation

    doi: 10.1038/s41467-024-49728-6

    Figure Lengend Snippet: A LSP DNA labeled with a donor/acceptor dye pair for single-molecule FRET (smFRET) assay. B Schematic of smFRET assay to study real-time, single-molecule DNA bending dynamics of TFAM. C , D , G A sample smFRET time trace (left) and FRET histogram (right) for LSP DNA alone (N Trace = 288), LSP + TFAM (N Trace = 420), and LSP + TFAM C-tail mutant (ΔCT) (N Trace = 219), respectively. E FRET transition density plot (TDP) for LSP + TFAM, showing two-state kinetics. F Dwell time histograms of the low FRET state, i.e., P-state (left), and the high FRET state, i.e., F-state (right). Red curves indicate the fitted single- and double-exponential models for P- and F-state, respectively. H Ensemble FRET spectra, showing TFAM-induced DNA bending at the ensemble level in solution. I Diagram summarizes the two-state DNA bending kinetics of the LSP-TFAM complex. The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using vbFRET or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.

    Article Snippet: The forward and reverse rate constants (~24 s −1 and ~1 s −1 ) were calculated from the inverse of P-state and F-state mean dwell times (see Supplementary Table ). smFRET time traces were fitted with Hidden Markov Model using vbFRET or ebFRET MATLAB software packages to plot FRET histograms, TDP, and dwell time histograms in this figure.

    Techniques: Labeling, Smfret Assay, Mutagenesis, Software