active-set algorithm Search Results


graphpad prism v7.04  (GraphPad Software Inc)
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GraphPad Software Inc graphpad prism v7.04
Graphpad Prism V7.04, supplied by GraphPad Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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perl algorithm  (ActiveState Software Inc)
90
ActiveState Software Inc perl algorithm
DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written <t>PERL</t> algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.
Perl Algorithm, supplied by ActiveState Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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active set algorithm  (MathWorks Inc)
96
MathWorks Inc active set algorithm
DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written <t>PERL</t> algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.
Active Set Algorithm, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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custom-written perl algorithm  (ActiveState Software Inc)
90
ActiveState Software Inc custom-written perl algorithm
DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written <t>PERL</t> algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.
Custom Written Perl Algorithm, supplied by ActiveState Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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python recipe  (ActiveState Software Inc)
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ActiveState Software Inc python recipe
DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written <t>PERL</t> algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.
Python Recipe, supplied by ActiveState Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sequest algorithm, version 2.7  (Sage-N Research Inc)
90
Sage-N Research Inc sequest algorithm, version 2.7
DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written <t>PERL</t> algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.
Sequest Algorithm, Version 2.7, supplied by Sage-N Research Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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actilife software actigraph 2012  (ActiGraph llc)
90
ActiGraph llc actilife software actigraph 2012
DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written <t>PERL</t> algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.
Actilife Software Actigraph 2012, supplied by ActiGraph llc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written PERL algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.

Journal: Nucleic Acids Research

Article Title: Visualizing helicases unwinding DNA at the single molecule level

doi: 10.1093/nar/gkq173

Figure Lengend Snippet: DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written PERL algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.

Article Snippet: To identify and characterize the pauses and unwinding phases a custom-written PERL algorithm (ActiveState Software Inc.) was developed.

Techniques: Activity Assay