Decoding a DNA Sequence with Java

Overview & Concepts

Students will write a Java program to read a DNA sequence from either the keyboard or a text file. Then they will display the protein sequence that is produced. Students will simulate the mutation of a single location in the DNA sequence to determine the effects of that mutation. Finally, students will look for the locations of a specific DNA sequence.

Grade Level: 

Concepts Covered: 

Text files, Strings, ArrayLists, Classes, Objects, genetics, DNA sequencing, protein synthesis, mutations.

Prior Knowledge Required: 

Java programming with Strings, Files, and ArrayLists. DNA sequencing and protein synthesis.

Activity Notes

Days to Teach: 

5 Days (80 minute periods)

Materials: 

  • Java IDE
  • Computer
  • Programming Description sheet
  • Intro to DNA Basics PowerPoint

Teaching Tips / Activity Overview: 

  1. Students will look at the Intro and DNA Basics PowerPoint to review the process.
  2. We will the decode some simple DNA sequences, both valid and invalid, by hand.  We will also look at the different type of mutations that might occur and the effects on the protein sequence.  
  3. Students will create a Java program that will solve the four problems specified on the assignment sheet.  The most important step os the first program, since all other programs in this project reuse the concept of reading a DNA sequence, validating the sequence, and converting it to a protein sequence.

Assessment: 

  • Formative: Decoding DNA sequence and looking for mutations by hand. 
  • Summative: Programs.

Extensions: 

Student may go to the Ensembl Genome Browser and download the DNA sequence of a specific gene on a specific chromosome.  Extend the Java program to read this text file into their program an decode the DNA sequence into a protein sequence.

Resources: 

Acknowledgements: 

These teacher notes and resources were produced by Rorabaugh.

Academic Standards
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