3.7C Apply and evaluate basic computer operations and concepts.

Phylogenetic Trees, Part 1: Pairwise Alignment of Related DNA / Protein Sequences using the LCS Algorithm

This lesson is the 1st in a unit on constructing Phylogenetic Trees from DNA or Protein Sequences. Students build an Excel spreadsheet to model the simplest implementation of the LCS (Longest Common Subsequence) algorithm in order to calculate the degree of homology between 2 sequences. Read more about Phylogenetic Trees, Part 1: Pairwise Alignment of Related DNA / Protein Sequences using the LCS Algorithm

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Bioinformatics Using Basic Genomics Sequences

This activity will familiarize high school students on the importance of computational biology in today's world. By writing computer programs that use genomics sequence analysis, the student will have a better understanding of molecular biology and how the vast amount of data that is provided in multiple on-line databases can be simplified by a few lines of code. Read more about Bioinformatics Using Basic Genomics Sequences

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Blood Critters in GridWorld

Students will use the GridWorld case study to create BloodCritters that extend the Critter class. These BloodCritters will have two alleles for their blood types and will be able to reproduce, randomly giving their children one allele each. These two alleles will determine the child's blood type. The color of each critter will be determined based on the blood type. Read more about Blood Critters in GridWorld

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Decoding a DNA Sequence with Java

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. Read more about Decoding a DNA Sequence with Java

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Process Coding Sequences of Transcripts Lab

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. Read more about Process Coding Sequences of Transcripts Lab

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A Progression of Computer Science Problems with Bioinformatics as the Context

This activity, a question set for teaching basic computer science ideas via bioinformatics, provides a variety of problems that build on students abilities in both computer science and bioinformatics. The questions get progressively more difficult and build off previous problems although any could be used as a stand alone as well.  Read more about A Progression of Computer Science Problems with Bioinformatics as the Context

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Medical Problem Solving using OMIM

In this case study activity, students read about a disease in the Mennonite population and learn more about the disorder using OMIM.  Students will also be introduced to SNP analysis to visualize how the gene that is causing a disorder is found.  Students will also get the opportunity to see how mutations can be determined and the effect of these mutations. Read more about Medical Problem Solving using OMIM

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