DNA (deoxyribonucleic acid) is a molecule that carries the genetic information used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA has four building blocks called nucleotides: Adenin (A), Thymine (T), Guanin (G) and Cytosine (C). All the information in the DNA is stored as a code made up of these four chemical bases.
Sub-strings of a DNA sequence having length k are called k-mers. For example, the k-mers of length 4 (k = 4) of the sequence ”GATTACA” are shown in Figure 1. In this example, w refers to step size with which the sliding window is moved. With w = 1, the window moves 1 letter to the right at each step, so that the first k-mer starts at position 1 and the second starts at position 2 and so on. The usage data over the sequence ”GATTACA” in this case is [(GATT,1), (ATTA,1),(TTAC,1),(TACA,1)], where each couple represents a k-mer (k = 4) and its frequency of occurrence in this sequence. When w = 2, the first k-mer starts at position 1, the second k-mer starts at position 3, the third position starts at 5 but since there are fewer than k = 4 nuclotides left, the count stops. The usage data for this case is [(GATT,1), (TTAC,1)] .
Nucleotide usage bias refers to differences in the frequency of occurrence of different k-mers of nucleotides (for example, when k = 3, the usage bias is called codon bias and has many biological implications).
In this project, your goal is to create an application that computes nucleotide usage bias of k-mers of variable size and step size for a set of DNA sequences.
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