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You are here: Home / Resources / Teaching Materials / Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach / About

Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

This laboratory module is a modification of the original published on CourseSource with a focus on plant biology. In the final activity, students conduct a BLAST to compare histone protein sequences between Arabidopsis, moss and yeast.

Listed in Teaching Materials | resource by group Bring Bioinformatics to Your Biology Classroom

Version 1.0 - published on 29 May 2019 doi:10.25334/Q4H458 - cite this

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

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

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Description

 

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.

 

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).

 

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.

CourseSource Citation of original publication

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

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Tags

  1. Activity Length
  2. Adapted at NIBLSE
  3. Advanced
  4. algorithms
  5. Audience Level
  6. bioinformatics
  7. BLAST
  8. BLOSUM scoring matrix
  9. C1. Role of bioinformatics
  10. C2. Computational concepts
  11. C4. Bioinformatics tools
  12. C5. Data retrieval
  13. C8. Data types
  14. CourseSource
  15. FASTA
  16. incubators
  17. Instructional Setting
  18. introductory
  19. Lab
  20. Majors
  21. More than 1 hour
  22. multiple sequence alignment
  23. NCBI
  24. neighbor-joining distance matrix
  25. NIBLSE
  26. phylogenetics
  27. phylogram
  28. Plant and Fungal Evolution
  29. plant biology
  30. sequence similarity
  31. sequencing
  32. Teaching material
  33. Undergraduate

Notes

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

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