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Introductory Video and worksheets on Module 1 and 2 on "Sequence Similarity: An inquiry based and under the hood..."

Author(s): Alice Tarun

St. Lawrence University

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Summary:
The video walks the students to complete Module 1 and 2 on Sequence Similarly and Alignment adapted from Tapprich (2019) and Hudson Alpha that teaches these modules within the context of the SARS-COVID 2 virus.

Licensed under CC Attribution-NonCommercial-ShareAlike 4.0 International according to these terms

Version 1.0 - published on 31 May 2021 doi:10.25334/RSKV-D240 - cite this

Adapted from: Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses v 5.0

Keywords

  1. bioinformatics
  2. sequencing
  3. FASTA
  4. NCBI
  5. NIBLSE
  6. algorithms
  7. BLAST
  8. multiple sequence alignment
  9. sequence similarity
  10. BLOSUM scoring matrix
  11. CourseSource

Alignments

  1. Resource Type
  2. Audience Level
  3. Activity Length
  4. NIBLSE Core Competencies
  5. NIBLSE Status
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Description

To introduce Bioinformatics in my General Biology course, the two modules on sequence similarity and alignment were taught in lab. These modules supplemented concepts taught in the Genetics unit of my General Biology course. The modules and the accompanying worksheets were posted in the lab LMS (Sakai). This video resource and the accompanying PowerPoint slides walks the students to complete the modules and reduced their confusion, so they are able to work on the worksheets at their own time.

 

CourseSource Citation

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. https://doi.org/10.24918/cs.2019.5 

Tapprich, W. (2019). Sequence Similarity Resource Adaptation: Exploring Ebola Virus. Bring Bioinformatics to Your Biology Classroom, QUBES Educational Resources. doi:10.25334/Q47X63.

PowerPoint slides of module screenshots were adapted from a presentation by Hudson Alpha (http://hghelix.hudsonalpha.org/) on COVID-19 teaching resources.

Notes

  • Exercise Format
    • The single composite learning resource has been split out into multiple stand-alone modular exercises
    • Each modular exercise, student thought question worksheet, necessary FASTA sequences, and instructor’s solution key have been bundled into a single document along with a preface page with implementation instructions for the instructor
    • The goal of the updated exercise format is to allow for effortless implementation of subsections over multiple class sessions and to encourage implementation of select subsections that best align with course learning objectives for instructors that would like to use a subset of the modules
  • Copy edits and minor text choice modifications
  • Exercise title change to mirror the associated modules by Tapprich. (2019), which is based on Kleinschmit et al (2019).
  •  
  • Reference

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. https://doi.org/10.24918/cs.2019.5

Tapprich, W. (2019). Sequence Similarity Resource Adaptation: Exploring Ebola Virus. Bring Bioinformatics to Your Biology Classroom, QUBES Educational Resources. doi:10.25334/Q47X63.

PowerPoint slides of module screenshots were adapted from a presentation by Hudson Alpha (http://hghelix.hudsonalpha.org/) on COVID-19 teaching resources.

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