Finding an Open Reading Frame (ORF) in a DNA Sequence
Teacher Notes
Overview and concepts
Overview
Students create Java classes to parse a DNA sequence to find an Open Reading Frame.
Grade level
AP Computer Science
Java concepts covered
ArrayLists, classes, static methods, object methods, passing parameters, returning values from methods.
Prior knowledge required
Open Reading Frame (ORF)
In-frame sequence
DNA
Nucleotides
Codons
Java String methods
Activity notes
Time frame
 Reading: 30 minutes.
 Laboratory activity: 90 minutes.
Materials
 Java
 Java IDE
 DNA sequence to be used
 Rules for Open Reading Frames
Teaching Tips / Activity Overview
1. Depending on your students’ backgrounds, assign reading so that they will understand about
the transcription of an Open Reading Frame from a DNA sequence to messenger RNA followed
by translation to a protein. Explain start and stop codons and the rules that determine what
section of a DNA sequence constitute an Open Reading Frame.
2. Have students manually identify an ORF in a DNA sequence:
5' GGGATCGATGCCCCTTAAAGAGTTTACATATTGCTGGAGGCGTTAACCCCGGA 3´
3. Have students code a program to identify an Open Reading Frame in a sequence of DNA:
String DNAsequence =
"TACGCAATGCGTATCATTCTGCTGGGCGCTCCGGGCGCAGGTAAAGGTACTCAGGCTCAATTCATCATGGAGAAATACGGCATTCCGCAAATCTC
TACTGGTGACATGTTGCGCGCCGCTGTAAAAGCAGGTTCTGAGTTAGGTCTGAAAGCAAAAGAAATTATGGATGCGGGCAAGTTGGTGACTGAT
GAGTTAGTTATCGCATTACTCAAAGAACGTATCACACAGGAAGATTGCCGCGATGGTTTTCTGTTAGACGGGTTCCCGCGTACCATTCCTCAGGCA
GATGCCATGAAAGAAGCCGGTATCAAAGTTGATTATGTGCTGGAGTTTGATGTTCCAGACGAGCTGATTGTTGAGCGCATTGTCGGCCGTCGGGT
ACATGCTGCTTCAGGCCGTGTTTATCACGTTAAATTCAACCCACCTAAAGTTGAAGATAAAGATGATGTTACCGGTGAAGAGCTGACTATTCGTAA
AGATGATCAGGAAGCGACTGTCCGTAAGCGTCTTATCGAATATCATCAACAAACTGCACCATTGGTTTCTTACTATCATAAAGAAGCGGATGCAGG
TAATACGCAATATTTTAAACTGGACGGAACCCGTAATGTAGCAGAAGTCAGTGCTGAACTGGCGACTATTCTCGGTTAATTCTGGATGGCCTTATA
GCTAAGGCGGTTTAAGGCCGCCTTAGCTATTTCAAGTAAGAAGGGCGTAGTACCTACAAAAGGAGATTTGGCATGATGCAAAGCAAACCCGGCG
TATTAATGGTTAATTTGGGGACACCAGATGCTCCAACGTCGAAAGCTATCAAGCGTTATTTAGCTGAGTTTTTGAGTGACCGCCGGGTAGTTGATA
CTTCCCCATTGCTATGGTGGCCATTGCTGCATGGTGTTATTTTACCGCTTCGGTCACCACGTGTAGCAAAACTTTATCAATCCGTTTGGATGGAAGA
GGGCTCTCCTTTATTGGTTTATAGCCGCCGCCAGCAGAAAGCACTGGCAGCAAGAATGCCTGATATTCCTGTAGAATTAGGCATGAGCTATGGTTC
AC";
4. Require students to use ArrayLists and objects to accomplish this task. Have them develop the
program in steps: a) Parse the string to find stop and start codons. b) Create an object to record
the position of the start and stop codon and whether the codon is a start or stop codon. c)
Create an ArrayList of these objects. Each element will represent a start or stop codon.
d)Identify sequence(s) which start with a start codon, end with a stop codon, contain at least
300 nucleotides, and are in frame. e) Store all sequences that meet this criteria in an ArrayList
whose elements consist of objects made up of each sequence, the position of its start codon,
and the position of its stop codon. f) Create the appropriate toString methods to print the
original sequence and each ORF located in it. Report sequences in line widths of 80.
5. Here is an example of the expected output:
* Original Sequence
TACGCAATGCGTATCATTCTGCTGGGCGCTCCGGGCGCAGGTAAAGGTACTCAGGCTCAATTCATCATGGAGAAATACGG
CATTCCGCAAATCTCTACTGGTGACATGTTGCGCGCCGCTGTAAAAGCAGGTTCTGAGTTAGGTCTGAAAGCAAAAGAAA
TTATGGATGCGGGCAAGTTGGTGACTGATGAGTTAGTTATCGCATTACTCAAAGAACGTATCACACAGGAAGATTGCCGC
GATGGTTTTCTGTTAGACGGGTTCCCGCGTACCATTCCTCAGGCAGATGCCATGAAAGAAGCCGGTATCAAAGTTGATTA
TGTGCTGGAGTTTGATGTTCCAGACGAGCTGATTGTTGAGCGCATTGTCGGCCGTCGGGTACATGCTGCTTCAGGCCGTG
TTTATCACGTTAAATTCAACCCACCTAAAGTTGAAGATAAAGATGATGTTACCGGTGAAGAGCTGACTATTCGTAAAGAT
GATCAGGAAGCGACTGTCCGTAAGCGTCTTATCGAATATCATCAACAAACTGCACCATTGGTTTCTTACTATCATAAAGA
AGCGGATGCAGGTAATACGCAATATTTTAAACTGGACGGAACCCGTAATGTAGCAGAAGTCAGTGCTGAACTGGCGACTA
TTCTCGGTTAATTCTGGATGGCCTTATAGCTAAGGCGGTTTAAGGCCGCCTTAGCTATTTCAAGTAAGAAGGGCGTAGTA
CCTACAAAAGGAGATTTGGCATGATGCAAAGCAAACCCGGCGTATTAATGGTTAATTTGGGGACACCAGATGCTCCAACG
TCGAAAGCTATCAAGCGTTATTTAGCTGAGTTTTTGAGTGACCGCCGGGTAGTTGATACTTCCCCATTGCTATGGTGGCC
ATTGCTGCATGGTGTTATTTTACCGCTTCGGTCACCACGTGTAGCAAAACTTTATCAATCCGTTTGGATGGAAGAGGGCT
CTCCTTTATTGGTTTATAGCCGCCGCCAGCAGAAAGCACTGGCAGCAAGAATGCCTGATATTCCTGTAGAATTAGGCATG
AGCTATGGTTCAC
Start codon found at position 6
Start codon found at position 66
Start codon found at position 105
Start codon found at position 162
Start codon found at position 291
Stop codon found at position 648
Start codon found at position 657
Stop codon found at position 666
Stop codon found at position 741
Stop codon found at position 765
Start codon found at position 789
Stop codon found at position 822
Stop codon found at position 834
Stop codon found at position 849
Start codon found at position 888
Stop codon found at position 921
Stop codon found at position 1026
Stop codon found at position 1032
Stop codon found at position 1038
Start codon found at position 1044
ORF start position: 292 ORF end position: 651
ORF Sequence(s)
ATGAAAGAAGCCGGTATCAAAGTTGATTATGTGCTGGAGTTTGATGTTCCAGACGAGCTGATTGTTGAGCGCATTGTCGG
CCGTCGGGTACATGCTGCTTCAGGCCGTGTTTATCACGTTAAATTCAACCCACCTAAAGTTGAAGATAAAGATGATGTTA
CCGGTGAAGAGCTGACTATTCGTAAAGATGATCAGGAAGCGACTGTCCGTAAGCGTCTTATCGAATATCATCAACAAACT
GCACCATTGGTTTCTTACTATCATAAAGAAGCGGATGCAGGTAATACGCAATATTTTAAACTGGACGGAACCCGTAATGT
AGCAGAAGTCAGTGCTGAACTGGCGACTATTCTCGGTTAA
*/
Assessment
 Programs will be graded with respect to the correct output, the correct use of ArrayLists and
objects to solve the problem, and the algorithm used to determine ORFs.
Extensions
 Additional sequences can be obtained online and analyzed with the program.
 ORFs can be translated into messenger RNA.
 Messenger RNA can be translated into proteins.
Acknowledgments
This lesson and teacher notes were produced by Cynthia Lang, adapted from
1. University of Wisconsin BioWeb:
http://bioweb.uwlax.edu/GenWeb/Molecular/Theory/Translation/Translation_Problems/translation_probl
ems.htm
2. Bioinformatics Exercises, developed by Paul Craig, Department of Chemistry, Rochester Institute of
Technology:
http://media.wiley.com/product_data/excerpt/57/04712149/0471214957-3.pdf