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Bioinformatics

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence...

Learning Objectives
At the end of this lesson, students will be able to:
Define similarity in a non-biological and biological sense when provided with two strings of letters.

Quantify the similarity between two gene/protein sequences.

Explain how a substitution matrix is used to quantify similarity.

Calculate amino acid similarity scores using a scoring matrix.

Demonstrate how to access genomic data (e.g., from NCBI nucleotide and protein databases).

Demonstrate how to use bioinformatics tools to analyze genomic data (e.g., BLASTP), explain a simplified BLAST search algorithm including how similarity is used to perform a BLAST search, and how to evaluate the results of a BLAST search.

Create a nearest-neighbor distance matrix.

Create a multiple sequence alignment using a nearest-neighbor distance matrix and a phylogram based on similarity of amino acid sequences.

Use appropriate bioinformatics sequence alignment tools to investigate a biological question.