Process Coding Sequences of Transcripts Lab

Overview & Concepts

Students will complete a Java OOP program that consists of six classes which represent a Gene, a Transcript, and Dictionaries. The Dictionary classes can be used for DNA to RNA transcription and RNA to Protein translation. The Transcript class will contain methods to transcript a DNA coding sequence into an mRNA sequence and to translate an mRNA sequence into a protein. The Gene class contains Transcript objects.

Concepts Covered: 

  • Computer Science: OOP, constructors, methods, instance data, arrays, Lists, ArrayLists, dictionary
  • Bioinformatics: genetics, chromosomes, genes, DNA, RNA, mRNA, nucleobases (bases), DNA coding sequence, transcript, codon, protein, amino acid, enzyme, transcription, translation

Prior Knowledge Required: 

Students must be familiar with Object Oriented Programming including constructors, methods, instance data, inheritance, and abstract classes. They must also have a working knowledge of arrays, Lists, and ArrayLists.

Activity Notes

Days to Teach: 

Approximately three 90 minute periods.


  • Process Coding Sequences Assignment.doc - the student assignment.
  • Process Coding Sequences Javadocs folder - the Java Documentation for the assignment. index.html is the main page.
  • Process Coding Sequences Assignment Student folder - the student starter code (includes a JCreator project)
  • Process Coding Sequences Assignment Teacher folder - the completed project

Teaching Tips / Activity Overview: 

  1. Teacher introduces the Lab which includes
    • Discussion of the purpose, goals, and work products of the lab.
    • Review of the genetics concepts and definitions involved in DNA coding sequences, mRNA, proteins, transcription, and translation.
    • Introduction to the Dictionary Data Structure.
  2. Student use the Internet to research DNA-RNA complementary bases used in transcription, and codon-amino acid relationships used in translation.
  3. Students work on lab (programming assignment).  Each student is responsible for completing his own assignment.  Students may consult, but may not copy.
  4. Teacher will circulate in the classroom as students work and
    • Help students as appropriate.
    • Make sure that students stay engaged.
    • Ask questions to assess understanding.
    • Discuss common difficulties with the class as a whole.


  • Make Dictionary a concrete class.
  • Reduce the coding requirements by including more pre-written code in the student starter project.


  • Pre-assessment: none
  • Summative assessment: Teacher will observe student engagement during the programming.
  • Post-assessment: Completed programming assignments will be evaluated for adherence to the requirements specified in the assignment (90%) and programming style based on Checkstyle results (10%).


  • The Dictionary class can be expanded in various ways:
    • Methods could be added to make it more general including methods to add entries, remove entries, and determine if the entries include a specific key.
    • Entries could be maintained in sorted order.
  • DNA Coding sequences and mRNA could be displayed in groups or three (codons).
  • File Input/Output requirements have been minimized in this assignment.  Students could write code to process the chromosome21.txt file directly.
  • A GUI (Graphical User Interface) could be added to improve the user interface to the assignment.


These teacher notes and resources were produced by Robert Glen Martin.

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