| 1 | <p>This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools. The exercise utilizes simple paper models to help students understand matrices and algorithms prior to use of web-based computational tools. Students start the module by defining sequence similarity and then investigating how similarity can be quantitatively compared between two similar length proteins using a BLOSUM scoring matrix. Students then consider finding local regions of similarity between a sequence query and subjects within a large database using BLAST. Lastly, students practice accessing FASTA formatted sequence information via NCBI databases as they collect sequences for a multiple sequence alignment in order to generate a phylogenetic tree.</p> | 1 | <p>For many undergraduates, one of the most challenging exercises in the study of evolutionary biology is developing and testing evolutionary hypotheses using phylogenetic trees. In this series of modules, modified from Kleinschmit et al. (2019), students develop predictions about tree structure under different evolutionary hypotheses, and assemble data from FASTA-formatted sequence files and databases hosted by NCBI (The National Center for Biotechnology Information). They then use the free, user-friendly program MEGA X to align sequence data and construct simple trees to test their hypotheses. These modules cover a key learning objective in biology—application of bioinformatics tools to answer a real-life biological question. Specifically, they allow students the opportunity to combine their knowledge of tree-thinking, skills in database searching (NCBI), and experience in making phylogenies (MEGA) to answer inquiry-based research questions on a range of applied topics.</p> |
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