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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 rst 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 rst 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] Nucleotide usage bias refers to dierences in the frequency of occurrence of dierent k-mers of nucleotides (For example, when k = 3 this 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. 2 Data Format DNA sequences are often stored in a text le having a specic format called FASTA le. FASTA format is a text-based format for representing either nucleotide or amino acid sequences. The format allows for sequence names and comments to precede each sequence. Your program should be able to read all sequences from a FASTA le and compute the k-mer usage bias from all sequences in the le. 3 Requirements In this phase, you are required to implement the following classes: // This class represents a set of sequences. public class SequenceSet { // Constructor. public SequenceSet(); // Load sequences from FASTA file. public static SequenceSet load(String fileName); // Return the global usage over all sequences in the set. The word length is k and window step size is w. public Usage getUsage(int k, int w); // Return all sequences in the set in the same order they appear in the file. public LinkedList<Sequence> getSequences(); } // This class represents a single sequence. public class Sequence { // Constructor. public Sequence(String header, String seq); // Return the header of the sequence. public String getHeader(); public String getSeq(); // Return the usage for word length k and window step size w. public Usage getUsage(int k, int w); } // This class represents usage data at the sequence or sequence set level. public class Usage { // Constructor. public Usage(); // Add a kmer with the corresponding number of occurrences. public add(String kmer, int count); // Return the number of occurrences of kmer. public int getCount(String kmer); // Return all kmers with their count. public LinkedList<Pair<String, Integer>> getCounts(); } // This class represents a pair. This class must be used as it is without modifications. public class Pair<U, V> { public U first; public V second; public Pair(U first, V second) { [login to view URL] = first; [login to view URL] = second; } }