3 | <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> | 3 | <p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:11.0pt;
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| | 4 | font-family:Arial;color:black">This exercise was conducted in a sophomore level Plant and Fungal Biology course. I utilized most of exercise 1 and 2 from Adam Klenschmit’s publication. To tailor the lab for a plant biology course I replaced the comparison in exercise 2 between the chimpanzee and human with two comparisons: one between Arabidopsis and a moss species; the other between Arabidopsis and yeast. I also removed the “One Fish, Two Fish” example to shorten the exercise.<o:p></o:p></span></p>
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| | 6 | <p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:11.0pt;
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| | 7 | font-family:Arial;color:black"><o:p> </o:p></span></p>
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| | 9 | <p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:11.0pt;
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| | 10 | font-family:Arial;color:black">The goal for this activity was to demonstrate how bioinformatics is used to evaluate evolutionary relationships between plants.The week prior to completing this activity, students conducted a morphological comparison between bryophytes, vascular – seedless plants, angiosperms and gymnosperms. They had also read associated textbook chapters and discussed a paper about the evolution of land plants (de Vries and Archibald, 2018). <o:p></o:p></span></p>
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| | 12 | <p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:11.0pt;
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| | 13 | font-family:Arial;color:black"><o:p> </o:p></span></p>
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| | 15 | <p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:11.0pt;
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| | 16 | font-family:Arial;color:black">The activity was completed during a 3 hour lab session in a computer lab, and the activity was a little long for the time allotted.<o:p></o:p></span></p>
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| | 18 | <p><strong>CourseSource Citation of original publication</strong></p>
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| | 20 | <p>Kleinschmit, A., Brink, B., Roof, S., Goller, C., and Robertson, S.D. 2019. Sequence Similarity: An inquiry based and “under the hood” approach for incorporating molecular sequence alignment in introductory undergraduate biology courses. CourseSource. <a href="https://doi.org/10.24918/cs.2019.5">https://doi.org/10.24918/cs.2019.5</a></p> |
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