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#56, v4.0 Published:
#1247, v1.0 Published:

Title

Old VersionNew Version
1Bioinformatics - Investigating Sequence Similarity 1Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

Authors

Old VersionNew Version
1Adam Kleinschmit (Adams State University) 1Ami Erickson ()
2Benita Brink (Adams State University) 2Ami Erickson ()
3Steven Roof (Fairmont State University)   
4Komal Vig (Alabama State University)   
5Carlos Christopher Goller (North Carolina State University)   
6Sabrina Robertson (North Carolina State University)   
7Hayley Orndorf (University of Pittsburgh)   
8Benita Brink (Adams State University)   

Description

Old VersionNew Version
1<p>The following modules are from a pre-print version of the &quot;Sequence Similarity: An inquiry based and &quot;under the hood&quot; approach for incorporating molecular sequence alignment in introductory undergraduate biology courses&quot; learning resource accepted for publication in CourseSource, which is currently in press.</p>  1<p style="margin:0in;margin-bottom:.0001pt"><o:p>&nbsp;</o:p></p>
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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;
   4font-family:Arial;color:black">This exercise was conducted in a sophomore level Plant and Fungal Biology course.&nbsp; I utilized most of exercise 1 and 2 from Adam Klenschmit&rsquo;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 &ldquo;One Fish, Two Fish&rdquo; 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;
   7font-family:Arial;color:black"><o:p>&nbsp;</o:p></span></p>
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   9<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:11.0pt;
   10font-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 &ndash; 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;
   13font-family:Arial;color:black"><o:p>&nbsp;</o:p></span></p>
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   15<p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:11.0pt;
   16font-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. &nbsp;2019. Sequence Similarity: An inquiry based and &ldquo;under the hood&rdquo; 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>

Quote

Old VersionNew Version
1 1Plants may seem simple, but use ALL of your senses and "look" more closely.

Attachments

1 file — ./Updated version 4 files_11_21_18/S1. student_handout.docx 1 file — Bioinformatics Wkst_Plant Biology.docx
2 file — ./Updated version 4 files_11_21_18/S10. Zika_seqs_student.txt 2 file — Erickson_NIBLSEFMNTeachingNotes.docx
3 file — ./Updated version 4 files_11_21_18/S11. Vet_Med_seqs.txt 3 file — Exercise 2. Protein Alignment Hand Out.docx
4 file — ./Updated version 4 files_11_21_18/S2. instructor_solutions.docx 4 link — Sequence Similarity: An inquiry based and &quot;under the hood&quot; approach for incorporating molecular sequence alignment in introductory undergraduate biology courses | CourseSource
5 file — ./Updated version 4 files_11_21_18/S3. BLAST_handout.docx 5 file — publication_1264_1362/sequence_sim.JPG
6 file — ./Updated version 4 files_11_21_18/S4. MSA_handout.docx
7 file — ./Updated version 4 files_11_21_18/S5. neighbor_Joining_handout.docx
8 file — ./Updated version 4 files_11_21_18/S6. Cytochrome_C_seqs.txt
9 file — ./Updated version 4 files_11_21_18/S7. ADH2_seqs_instructor.txt
10 file — ./Updated version 4 files_11_21_18/S8. ADH2_seqs_student.txt
11 file — ./Updated version 4 files_11_21_18/S9. Zika_seqs_instructor.txt
12 file — ./sequence_sim.JPG