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Bioinformatics - Investigating Sequence Similarity

Author(s): Adam Kleinschmit1, Benita Brink1, Steven Roof2, Komal Vig3

1. Adams State University 2. Hampshire College 3. Alabama 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 Creative Commons CC0 1.0 Universal

Version 1.0 - published on 31 Jan 2017 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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Description

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.

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