Ryan K. Shultzaberger

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Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy,(More)
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base −7, rather than −11, of the −10 may be flipping to initiate transcription. We found that the sequence conservation of σ 70 binding sites is 6.5 ± 0.1 bits. Some(More)
Information theory was used to build a promoter model that accounts for the À10, the À35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base À7, rather than À11, of the À10 may be flipping to initiate transcription. We found that the sequence conservation of s 70 binding sites is 6.5 ± 0.1 bits. Some(More)
Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur binding, which was then refined by adding 13 experimentally confirmed sites. When the refined model was scanned across all available footprinted sequences, sequence(More)
Sequence logos: A new way to display consensus sequences. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. Visual display of sequence conservation as an aid to taxonomic classification using PCR amplification. information conservation implies that at least three proteins bind independently to(More)
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