Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction part of Teaching Genomics at Small Colleges:Genomics Instructional Units Minicollection
This laboratory exercise is a guided discovery of computational methods for comparing protein sequences. It accompanies several weeks of wet lab work in which students clone cDNAs encoding Cytochrome P450 1A (CYP1A) from animals (primarily fish) collected locally and exposed to pollution compounds that induce expression of the enzyme. In this exercise, students perform BLAST searches of reported CYP1A sequences and construct phylogenetic trees using CYP1A amino acid sequences from various vertebrate species, especially those with multiple CYP1A paralogs. These guided discovery activities prepare students for subsequent analyses of novel cDNA sequences that they clone.