We will be discussing the problem of motif definition, search and quantification in DNA sequences. Starting from the concept of a DNA motif we will be covering the concepts of consensus sequences and the probabilistic definition of motifs as PWM and PSSM tables.We will then discuss the concept of information based on Claude Shannon's theory of Entropy and implement algorithms for:
a. the construction of a motif's PWM and PSSM
b. the search of a sequence for a specific motif given its PWM/PSSM
c. the calculation of a motif's information content through Entropy calculations
d. the representation of a motif as a sequence logo