1887

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

    Authors: Peter D. Newell1, Ashwana D. Fricker2, Constance Armanda Roco2, Pete Chandrangsu2, Susan M. Merkel2,*
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    Affiliations: 1: Departments of Entomology, Cornell University, Ithaca, NY 14853; 2: Microbiology, Cornell University, Ithaca, NY 14853
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 02 December 2013
    • Supplemental materials available at http://jmbe.asm.org
    • *Corresponding author. Mailing address: Department of Microbiology, 111 Wing Hall, Cornell University, Ithaca, NY 14853. Phone: 607-254-2767. Fax: 607-255-3904. E-mail: smm3@cornell.edu.
    • ©2013 Author(s). Published by the American Society for Microbiology.
    Source: J. Microbiol. Biol. Educ. December 2013 vol. 14 no. 2 238-243. doi:10.1128/jmbe.v14i2.637
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    Abstract:

    As biological sequence data are generated at an ever increasing rate, the role of bioinformatics in biological research also grows. Students must be trained to complete and interpret bioinformatic searches to enable them to effectively utilize the trove of sequence data available. A key bioinformatic tool for sequence comparison and genome database searching is BLAST (Basic Local Alignment Search Tool). BLAST identifies sequences in a database that are similar to the entered query sequence, and ranks them based on the length and quality of the alignment. Our goal was to introduce sophomore and junior level undergraduate students to the basic functions and uses of BLAST with a small group activity lasting a single class period. The activity provides students an opportunity to perform a BLAST search, interpret the data output, and use the data to make inferences about bacterial cell envelope structure. The activity consists of two parts. Part 1 is a handout to be completed prior to class, complete with video tutorial, that reviews cell envelope structure, introduces key terms, and allows students to familiarize themselves with the mechanics of a BLAST search. Part 2 consists of a hands-on, web-based small group activity to be completed during the class period. Evaluation of the activity through student performance assessments suggests that students who complete the activity can better interpret the BLAST output parameters % query coverage and % max identity. While the topic of the activity is bacterial cell wall structure, it could be adapted to address other biological concepts.

Key Concept Ranking

Outer Membrane Proteins
0.525
Bacteria and Archaea
0.47414687
Bacterial Cell Wall
0.46661684
Amino Acids
0.4275676
Bacterial Cell Structure
0.4242893
Pseudomonas aeruginosa
0.38943338
0.525

References & Citations

1. American Association for the Advancement of Science2010Vision and change in undergraduate biology education: a call to action. A report of the American Association for the Advancement of Science[Online.] http://visionandchange.org/
2. DeHaan RL2005The impending revolution in undergraduate science educationJ Sci Educ Teach1425326910.1007/s10956-005-4425-3 http://dx.doi.org/10.1007/s10956-005-4425-3
3. Ditty JL, et al2010Incorporating genomics and bioinformatics across the life sciences curriculumPLoS Biol8e100044810.1371/journal.pbio.1000448207114782919421 http://dx.doi.org/10.1371/journal.pbio.1000448
4. Kerfeld CA, Scott KMUsing BLAST to Teach “E-value-tionary”Concepts PloS Biol9e1001014
5. Klein JR, Gulsvig T2012Using bioinformatics to develop and test hypotheses: E. coli-specific virulence determinantsJ. Microbiol. Biol. Educ13161169236538043577336
6. May JB2013Engaging students in a bioinformatics activity to introduce gene structure and functionJ Microbiol Biol Educ14107109238583613706140
7. National Research Council2003Bio2010: Transforming Undergraduate Education for Future Research BiologistsThe National Academies PressWashington, DC[Online.] http://www.nap.edu/openbook.php?isbn=0309085357
8. National Research Council2009A new biology for the 21st century: ensuring the United States leads the coming biology revolutionThe National Academies PressWashington, DC[Online.] http://www.nap.edu/catalog.php?record_id=12764
9. Ranganathan S2005Bioinformatics education— Perspectives and challengesPLoS Comput Biol1e5210.1371/journal.pcbi.0010052 http://dx.doi.org/10.1371/journal.pcbi.0010052
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/content/journal/jmbe/10.1128/jmbe.v14i2.637
2013-12-02
2017-11-21

Abstract:

As biological sequence data are generated at an ever increasing rate, the role of bioinformatics in biological research also grows. Students must be trained to complete and interpret bioinformatic searches to enable them to effectively utilize the trove of sequence data available. A key bioinformatic tool for sequence comparison and genome database searching is BLAST (Basic Local Alignment Search Tool). BLAST identifies sequences in a database that are similar to the entered query sequence, and ranks them based on the length and quality of the alignment. Our goal was to introduce sophomore and junior level undergraduate students to the basic functions and uses of BLAST with a small group activity lasting a single class period. The activity provides students an opportunity to perform a BLAST search, interpret the data output, and use the data to make inferences about bacterial cell envelope structure. The activity consists of two parts. Part 1 is a handout to be completed prior to class, complete with video tutorial, that reviews cell envelope structure, introduces key terms, and allows students to familiarize themselves with the mechanics of a BLAST search. Part 2 consists of a hands-on, web-based small group activity to be completed during the class period. Evaluation of the activity through student performance assessments suggests that students who complete the activity can better interpret the BLAST output parameters % query coverage and % max identity. While the topic of the activity is bacterial cell wall structure, it could be adapted to address other biological concepts.

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