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#56, v1.0 Published:
#1317, v1.0 Published:

Title

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1Bioinformatics - Investigating Sequence Similarity 1Sequence Similarity in Developmental Biology - A Bioinformatics Exercise Using Myostatin

Authors

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1Adam Kleinschmit (Adams State University) 1Barbara Murdoch ()
2Benita Brink (Adams State University) 2Barbara Murdoch ()
3Steven Roof (Hampshire College)   
4Komal Vig (Alabama State University)   
5Hayley Orndorf (University of Pittsburgh)   

Description

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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>This exercise integrates bioinformatics with developmental biology, and provides an introduction regarding how to use bioinformatics to assess sequence similarities. The implications of these similarities provides students with a basic understanding of how model organisms can provide useful information regarding human health and disease.</p>

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Attachments

1 file — Adam Kleinschmit - BLAST activity Sequence Alignment.docx 1 file — 1.Murdoch_NIBLSEFMNTeachingNotesTemplateSp19.docx
2 file — Adam Kleinschmit - CytochromC Protein Seq MSA.txt 2 file — 2. Student handout_Murdoch_Similarity in Developmental Biology.docx
3 file — Adam Kleinschmit - handout MSA calculation sheet.docx 3 file — 3. S3. BLAST_handout_Kleinschmit et al.docx
4 file — Adam Kleinschmit - Lab 11 Bioinformatics Activity Oct2016.docx 4 file — 4. TGF-b signaling pathway.pptx
5 file — Adam Kleinschmit - sequence Similarity in Bioinformatics.docx 5 file — 5. Bioinformatics_BIO 434 WORKSHEET_vfinal2.docx
6 file — Adam Kleinschmit - Solutions Bioinformatics Lab.docx 6 file — 5.1. Bioinformatics_BIO 434 WORKSHEET answers_vfinal2.docx
7 file — ./sequence_sim.JPG 7 link — Sequence Similarity: An inquiry based and &quot;under the hood&quot; approach for incorporating molecular sequence alignment in introductory undergraduate biology courses | CourseSource
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