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Bioinformatics - Investigating Sequence Similarity

Author(s): Adam Kleinschmit1, Benita Brink1, Steven Roof2, Carlos Christopher Goller3, Sabrina Robertson3

1. Adams State University 2. Fairmont State University 3. North Carolina State University

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Adapt 8
Summary:
This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

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

Version 4.0 - published on 04 Dec 2018 doi:10.25334/Q4VM1P - cite this Last public release: 5.0

Keywords

  1. phylogenetics
  2. bioinformatics
  3. sequencing
  4. FASTA
  5. NCBI
  6. NIBLSE
  7. algorithms
  8. incubators
  9. BLAST
  10. multiple sequence alignment
  11. sequence similarity
  12. BLOSUM scoring matrix
  13. neighbor-joining distance matrix
  14. CourseSource
  15. phylogram
  16. Zika virus

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

The following modules are from a pre-print version of the "Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses" learning resource accepted for publication in CourseSource, which is currently in press.

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.

Notes

The learning resource was modified to provide further background information for the reader in addition to an expanded paper-based distance matrix exercise and a set of inquiry questions now bookend the resource to promote student engagement and application of the concepts explored.

This version includes an updated author list. 

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