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Title

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1Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses 1Sequence Similarity: Introducing Biological Databases to Community College Biology Students

Authors

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1Sabrina Robertson (North Carolina State University) 1Jennifer Katcher ()
2Carlos Christopher Goller (North Carolina State University) 2Jennifer Katcher ()
3Steven Roof (Fairmont State University)   
4Benita Brink (Adams State University)   
5Adam Kleinschmit (Adams State University)   
6Hayley Orndorf (University of Pittsburgh)   

Description

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1<p>Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does &quot;under the hood.&quot; A solid understanding of how a bioinformatics computational algorithm functions, including its limitations, is key for interpreting the output in a biologically relevant context. This introductory bioinformatics exercise integrates an introduction to web-based sequence alignment algorithms with models to facilitate student reflection and appreciation for how computational tools provide similarity output data. The exercise concludes with a set of inquiry-based questions in which students may apply computational tools to solve a real biological problem.</p>  1<p>Most introductory biology students at a 2 year school have not used biological databases. Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does &quot;under the hood.&quot; A solid understanding of how a bioinformatics computational algorithm functions, including its limitations, is key for interpreting the output in a biologically relevant context. This introductory bioinformatics exercise integrates an introduction to web-based sequence alignment algorithms with models to facilitate student reflection and appreciation for how computational tools provide similarity output data. The exercise concludes with a set of inquiry-based questions in which students may apply computational tools to solve a real biological problem.</p>
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3<p>In the module, students first define sequence similarity and then investigate how similarity can be quantitatively compared between two similar length proteins using a Blocks Substitution Matrix (BLOSUM) scoring matrix. Students then look for local regions of similarity between a sequence query and subjects within a large database using Basic Local Alignment Search Tool (BLAST). Lastly, students access text-based FASTA-formatted sequence information via National Center for Biotechnology Information (NCBI) databases as they collect sequences for a multiple sequence alignment using Clustal Omega to generate a phylogram and evaluate evolutionary relationships. The combination of diverse, inquiry-based questions, paper models, and web-based computational resources provides students with a solid basis for more advanced bioinformatics topics and an appreciation for the importance of bioinformatics tools across the discipline of biology.</p>  3<p>In the module, students first define sequence similarity and then investigate how similarity can be quantitatively compared between two similar length proteins using a Blocks Substitution Matrix (BLOSUM) scoring matrix. Students then look for local regions of similarity between a sequence query and subjects within a large database using Basic Local Alignment Search Tool (BLAST). Lastly, students access text-based FASTA-formatted sequence information via National Center for Biotechnology Information (NCBI) databases as they collect sequences for a multiple sequence alignment using Clustal Omega to generate a phylogram and evaluate evolutionary relationships. The combination of diverse, inquiry-based questions, paper models, and web-based computational resources provides students with a solid basis for more advanced bioinformatics topics and an appreciation for the importance of bioinformatics tools across the discipline of biology.</p>  
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Quote

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1 1Your students will appreciate how quickly computers can align sequences after trying to do it themselves!

Attachments

1 link — Sequence Similarity: An inquiry based and &quot;under the hood&quot; approach for incorporating molecular sequence alignment in introductory undergraduate biology courses | CourseSource 1 link — Sequence Similarity: An inquiry based and &quot;under the hood&quot; approach for incorporating molecular sequence alignment in introductory undergraduate biology courses | CourseSource
2 file — ./sequence_sim.JPG 2 file — publication_1264_2599/sequence_sim.JPG
3 file — Katcher_Exercise_1/Ex1_Teaching_notes_Katcher.docx
4 file — Katcher_Exercise_1/Exercise_1_accompanying_slides.pptx
5 file — Katcher_Exercise_1/Exercise_1_Discussion_Questions.docx
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