Developing an Application for Computing Nucleotide Usage Bias

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 composition count in this case is [GATT=1, ATTA=1,TTAC=1,TACA=1]. 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 composition count for this case is [GATT=1, TTAC=1] .