Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics
Familiarity with genome-scale data and the bioinformatic skills to analyze it have become essential for understanding and advancing modern biology and human health, yet many undergraduate biology majors are never exposed to hands-on bioinformatics. This paper presents a module that introduces studen...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.578859/full |
| _version_ | 1818870389600681984 |
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| author | Katherine Lynn Petrie Katherine Lynn Petrie Rujia Xie |
| author_facet | Katherine Lynn Petrie Katherine Lynn Petrie Rujia Xie |
| author_sort | Katherine Lynn Petrie |
| collection | DOAJ |
| description | Familiarity with genome-scale data and the bioinformatic skills to analyze it have become essential for understanding and advancing modern biology and human health, yet many undergraduate biology majors are never exposed to hands-on bioinformatics. This paper presents a module that introduces students to applied bioinformatic analysis within the context of a research-based microbiology lab course. One of the most commonly used genomic analyses in biology is resequencing: determining the sequence of DNA bases in a derived strain of some organism, and comparing it to the known ancestral genome of that organism to better understand the phenotypic differences between them. Many existing CUREs — Course Based Undergraduate Research Experiences — evolve or select new strains of bacteria and compare them phenotypically to ancestral strains. This paper covers standardized strategies and procedures, accessible to undergraduates, for preparing and analyzing microbial whole-genome resequencing data to examine the genotypic differences between such strains. Wet-lab protocols and computational tutorials are provided, along with additional guidelines for educators, providing instructors without a next-generation sequencing or bioinformatics background the necessary information to incorporate whole-genome sequencing and command-line analysis into their class. This module introduces novice students to running software at the command-line, giving them exposure and familiarity with the types of tools that make up the vast majority of open-source scientific software used in contemporary biology. Completion of the module improves student attitudes toward computing, which may make them more likely to pursue further bioinformatics study. |
| first_indexed | 2024-12-19T12:06:15Z |
| format | Article |
| id | doaj.art-4296e6e28a694c91b2bfb0deabffb694 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-19T12:06:15Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-4296e6e28a694c91b2bfb0deabffb6942022-12-21T20:22:20ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-03-011210.3389/fmicb.2021.578859578859Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line BioinformaticsKatherine Lynn Petrie0Katherine Lynn Petrie1Rujia Xie2Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United StatesEarth-Life Science Institute, Tokyo Institute of Technology, Tokyo, JapanDivision of Biological Sciences, University of California, San Diego, La Jolla, CA, United StatesFamiliarity with genome-scale data and the bioinformatic skills to analyze it have become essential for understanding and advancing modern biology and human health, yet many undergraduate biology majors are never exposed to hands-on bioinformatics. This paper presents a module that introduces students to applied bioinformatic analysis within the context of a research-based microbiology lab course. One of the most commonly used genomic analyses in biology is resequencing: determining the sequence of DNA bases in a derived strain of some organism, and comparing it to the known ancestral genome of that organism to better understand the phenotypic differences between them. Many existing CUREs — Course Based Undergraduate Research Experiences — evolve or select new strains of bacteria and compare them phenotypically to ancestral strains. This paper covers standardized strategies and procedures, accessible to undergraduates, for preparing and analyzing microbial whole-genome resequencing data to examine the genotypic differences between such strains. Wet-lab protocols and computational tutorials are provided, along with additional guidelines for educators, providing instructors without a next-generation sequencing or bioinformatics background the necessary information to incorporate whole-genome sequencing and command-line analysis into their class. This module introduces novice students to running software at the command-line, giving them exposure and familiarity with the types of tools that make up the vast majority of open-source scientific software used in contemporary biology. Completion of the module improves student attitudes toward computing, which may make them more likely to pursue further bioinformatics study.https://www.frontiersin.org/articles/10.3389/fmicb.2021.578859/fullCUREbioinformaticsbioinformatics tutorialresequencingbreseqnext-generation sequencing |
| spellingShingle | Katherine Lynn Petrie Katherine Lynn Petrie Rujia Xie Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics Frontiers in Microbiology CURE bioinformatics bioinformatics tutorial resequencing breseq next-generation sequencing |
| title | Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics |
| title_full | Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics |
| title_fullStr | Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics |
| title_full_unstemmed | Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics |
| title_short | Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics |
| title_sort | resequencing of microbial isolates a lab module to introduce novices to command line bioinformatics |
| topic | CURE bioinformatics bioinformatics tutorial resequencing breseq next-generation sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.578859/full |
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