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Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

Author(s): Ami Erickson

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Summary:
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.

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

Version 1.0 - published on 29 May 2019 doi:10.25334/Q4H458 - 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. phylogenetics
  2. bioinformatics
  3. sequencing
  4. FASTA
  5. NCBI
  6. plant biology
  7. NIBLSE
  8. algorithms
  9. incubators
  10. Plant and Fungal Evolution
  11. BLAST
  12. multiple sequence alignment
  13. sequence similarity
  14. BLOSUM scoring matrix
  15. neighbor-joining distance matrix
  16. CourseSource
  17. phylogram

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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

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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