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A Small-Group Activity Introducing the Use and Interpretation of BLAST.

Peter D Newell1, Ashwana D Fricker2, Constance Armanda Roco2

  • 1Departments of Entomology, Cornell University, Ithaca, NY 14853.

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|December 21, 2013
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Summary

This study introduces undergraduate students to Basic Local Alignment Search Tool (BLAST) bioinformatics searches. Students learned to interpret BLAST results for analyzing bacterial cell envelope structure.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Biological sequence data generation is increasing rapidly.
  • Bioinformatics is crucial for biological research and requires trained students.
  • Basic Local Alignment Search Tool (BLAST) is a key tool for sequence comparison and database searching.

Purpose of the Study:

  • To introduce undergraduate students to the functions and uses of BLAST.
  • To provide hands-on experience with BLAST searches and data interpretation.
  • To enable students to make inferences about bacterial cell envelope structure using BLAST.

Main Methods:

  • A two-part activity was designed for a single class period.
  • Part 1 involved a pre-class handout with a video tutorial on cell envelopes and BLAST mechanics.
  • Part 2 was a hands-on, web-based small group activity using BLAST.

Main Results:

  • Students who completed the activity showed improved interpretation of BLAST output parameters.
  • Specifically, students better understood % query coverage and % max identity.
  • The activity successfully facilitated learning about bacterial cell envelope structure.

Conclusions:

  • The developed BLAST activity is effective for teaching bioinformatics to undergraduates.
  • The activity enhances students' ability to interpret sequence similarity search results.
  • The curriculum can be adapted for various biological concepts beyond bacterial cell envelopes.