1887

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

    Author: Paul A. Jensen1
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    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: pjens@illinois.edu.
    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.2016An introduction to next-generation sequencing technologySan Diego, CAAvailable at: http://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf. Retrieved January 1, 2017
2. Haenni M, Moreillon P2006Mutations in penicillin-binding protein (PBP) genes and in non-PBP genes during selection of penicillin-resistant Streptococcus gordoniiAntimicrob Agents Chemother50124053406110.1128/AAC.00676-06170007411693971 http://dx.doi.org/10.1128/AAC.00676-06
3. Walker FO2007Huntington’s diseaseLancet369955721822810.1016/S0140-6736(07)60111-117240289 http://dx.doi.org/10.1016/S0140-6736(07)60111-1
4. Markowetz F2017All biology is computational biologyPLOS Biol153e200205010.1371/journal.pbio.2002050282781525344307 http://dx.doi.org/10.1371/journal.pbio.2002050
5. Ellis J, Fosdick BK, Rasmussen C2016Women 1.5 times more likely to leave STEM pipeline after calculus compared to men: lack of mathematical confidence a potential culpritPLOS One117e015744710.1371/journal.pone.0157447274102624943602 http://dx.doi.org/10.1371/journal.pone.0157447
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/content/journal/jmbe/10.1128/jmbe.v18i2.1295
2017-06-09
2017-07-28

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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