Lab 4: Gene Detection

Task Outline

• Due Date: Friday, October 18, 2019
• Total Points: 10
• Implement a Java program that determines which gene is present in a DNA sequence.

Background Theory

• DNA is often described as a double helix of molecules known as nucleotides. Only four DNA nucleotides exist, and they are known by the labels A, C, G, and T. This means that we can conveniently represent a DNA sequence with a Java text string.
• A cluster of three nucleotides is called a codon, and they represent amino acids which are present in DNA. For example, ATG is a codon which occurs throughout a DNA sequence. Codons are significant, because they are markers which indicate the presence of a gene.
• ATG is the start codon which marks the beginning of a gene sequence. All of the nucleotides which are present, right up to, and including the stop codon are part of the gene.

Example Case

• Consider the following DNA sequence: ATATGTAGCTAGCATAATA
• The start codon is ATG, and the stop codon for this example is TAA. Note that there are 9 nucleotides between these codons: AT ATGTAGCTAGCATAA TA
• Therefore, the gene sequence which results from these codons is: ATGTAGCTAGCATAA

Hints

• Note that we will not consider the case where a gene is absent from a DNA sequence. All of the DNA sequences used in the test benches have exactly one gene for you to find.
• Also, each of the DNA sequences will have exactly one stop codon for your program to locate. In other words, there will not be multiple stop codons in the gene sequences.

Code Distribution

Description	File Size	File Name
Java Source Code for Gene Detection	5.2KB	lab04.zip

Contents of lab04.zip:

Lab04GeneDetection/
├── GeneDetection.class
├── GeneDetection.ctxt
├── GeneDetection.java
├── GeneDetectionJUnitTest.class
├── GeneDetectionJUnitTest.ctxt
├── GeneDetectionJUnitTest.java
├── package.bluej
└── README.TXT

Specification

• Write a Java program in the file GeneDetection.java that finds and displays a single gene which is present in a DNA sequence.
• You will write your solution in a function called findGene(String dna, String stopCodon) right below the place where it says: YOUR CODE HERE
• When the function call findGene("ATATGTAGCTAGCATAATA", "TAA") is executed, the output of the program should be: ATGTAGCTAGCATAA

Testing

• Click on the Run Tests button to execute the JUnit test bench. JUnit indicates a successful test with a green bar, and an unsuccessful test with a red bar.

Submission

• Upload the file GeneDetection.java to the Web-CAT automated grading platform.