This class will focus on aspects of sequence (primarily genomic) composition and problems related to its analysis, which will serve as an introductory "warm-up" to algorithms. We will be discussing the problem of calculating the GC% of a given sequence, its comparison to that of another species and ways to detect outlier regions in terms of genomic in a given genome.
Algorithms that we will be discussing include:
a.calculating the GC% of a DNA sequence
b. the computation of k-mer frequencies from a DNA sequence
c. locating candidate regions of horizontal gene transfer based on k-mer frequencies
d. the definition of a sequence's origin of replication based on sequence composition.