Ab initio predictions of transcription factor binding

Joel Bader
Johns Hopkins University

Gene regulation depends on transcription factor proteins that recognize specific DNA sequences. We are developing computational methods to calculate the recognized DNA sequence purely from the transcription factor protein sequence and homology modeling of the protein-DNA complex. Predictions are ab initio in that they do not rely on analysis of promoters of presumably co-regulated genes. The long-term goal of this project is to predict the regulatory protein- DNA interactions of an organism purely from its genome sequence. We will describe initial results with homeodomain and leucine zipper protein families.

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