1887

Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics

    Author: Paul A. Jensen1
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 04 January 2017 Accepted 13 March 2017 Published 09 June 2017
    • ©2017 Author(s). Published by the American Society for Microbiology.
    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.

    • Supplemental materials available at http://asmscience.org/jmbe
    • Corresponding author. Mailing address: Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, 1270 Digital Computer Laboratory, MC-278, University of Illinois at Urbana-Champaign, Urbana, IL, 61801. Phone: 217-333-1867. Email: [email protected].
    Source: J. Microbiol. Biol. Educ. June 2017 vol. 18 no. 2 doi:10.1128/jmbe.v18i2.1295
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    Abstract:

    The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly process using short DNA sequences printed on paper. Topics highlighted during the lesson include overlap identification, reference sequences, and the challenges arising from sequencing errors, low-frequency mutations, and repetitive regions. Sample materials provide reads and solutions for assembling clinically relevant regions of the S. gordonii penicillin binding protein and the human HTT gene. An online tool allows instructors to generate custom read sets from other DNA sequences.

Key Concept Ranking

Sanger Sequencing
0.54545456
Streptococcus gordonii
0.52049595
Antimicrobial Resistance
0.49259457
DNA
0.48796493
0.54545456

References & Citations

1. Illumina, Inc. 2016 An introduction to next-generation sequencing technology San Diego, CA Available at: http://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf. Retrieved January 1, 2017
2. Haenni M, Moreillon P 2006 Mutations in penicillin-binding protein (PBP) genes and in non-PBP genes during selection of penicillin-resistant Streptococcus gordonii Antimicrob Agents Chemother 50 12 4053 4061 10.1128/AAC.00676-06 17000741 1693971 http://dx.doi.org/10.1128/AAC.00676-06
3. Walker FO 2007 Huntington’s disease Lancet 369 9557 218 228 10.1016/S0140-6736(07)60111-1 17240289 http://dx.doi.org/10.1016/S0140-6736(07)60111-1
4. Markowetz F 2017 All biology is computational biology PLOS Biol 15 3 e2002050 10.1371/journal.pbio.2002050 28278152 5344307 http://dx.doi.org/10.1371/journal.pbio.2002050
5. Ellis J, Fosdick BK, Rasmussen C 2016 Women 1.5 times more likely to leave STEM pipeline after calculus compared to men: lack of mathematical confidence a potential culprit PLOS One 11 7 e0157447 10.1371/journal.pone.0157447 27410262 4943602 http://dx.doi.org/10.1371/journal.pone.0157447

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2017-06-09
2019-07-17

Abstract:

The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly process using short DNA sequences printed on paper. Topics highlighted during the lesson include overlap identification, reference sequences, and the challenges arising from sequencing errors, low-frequency mutations, and repetitive regions. Sample materials provide reads and solutions for assembling clinically relevant regions of the S. gordonii penicillin binding protein and the human HTT gene. An online tool allows instructors to generate custom read sets from other DNA sequences.

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FIGURE 1

Paper DNA “short reads” assembled by high school students.

Source: J. Microbiol. Biol. Educ. June 2017 vol. 18 no. 2 doi:10.1128/jmbe.v18i2.1295
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