Transcription Factor binding to DNA binding sites is one of the primary causes of generegulation. A common representation of transcription factor binding sites is at the DNAsequence level, partly due to reoccurring patterns at the sequence level that occur throughoutthe genome for a given factor. The first chapter of this dissertation introduces gene regulationfrom the perspective of development. In addition the mathematical-physics foundation forperforming calculations and for representations of the transcription factor binding sites atthe sequence level is discussed in Chapter 1. In Chapter 2 I explore the possibility thattwo distinct sub-types of binding sites may co-exist within a population of functional sites.This leads to a model that can be used for prediction of transcription factor binding sites.In Chapter 3 I explore modelling of Dorsal Ventral early development Gene RegulatoryNetwork, using the tools built up in Chapter 1 and 2, namely 'Position Weight Matrices'that allow for prediction of binding energies for genomic segments of DNA.
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