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: [email protected].
    • ©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 Science 2010 Vision 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 RL 2005 The impending revolution in undergraduate science education J Sci Educ Teach 14 253 269 10.1007/s10956-005-4425-3 http://dx.doi.org/10.1007/s10956-005-4425-3
3. Ditty JL, et al 2010 Incorporating genomics and bioinformatics across the life sciences curriculum PLoS Biol 8 e1000448 10.1371/journal.pbio.1000448 20711478 2919421 http://dx.doi.org/10.1371/journal.pbio.1000448
4. Kerfeld CA, Scott KM Using BLAST to Teach “E-value-tionary” Concepts PloS Biol 9 e1001014
5. Klein JR, Gulsvig T 2012 Using bioinformatics to develop and test hypotheses: E. coli-specific virulence determinants J. Microbiol. Biol. Educ 13 161 169 23653804 3577336
6. May JB 2013 Engaging students in a bioinformatics activity to introduce gene structure and function J Microbiol Biol Educ 14 107 109 23858361 3706140
7. National Research Council 2003 Bio2010: Transforming Undergraduate Education for Future Research Biologists The National Academies Press Washington, DC [Online.] http://www.nap.edu/openbook.php?isbn=0309085357
8. National Research Council 2009 A new biology for the 21st century: ensuring the United States leads the coming biology revolution The National Academies Press Washington, DC [Online.] http://www.nap.edu/catalog.php?record_id=12764
9. Ranganathan S 2005 Bioinformatics education— Perspectives and challenges PLoS Comput Biol 1 e52 10.1371/journal.pcbi.0010052 http://dx.doi.org/10.1371/journal.pcbi.0010052

Supplemental Material

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/content/journal/jmbe/10.1128/jmbe.v14i2.637
2013-12-02
2019-10-21

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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