دورية أكاديمية
In silico Phage Hunting: Bioinformatics Exercises to Identify and Explore Bacteriophage Genomes.
| العنوان: | In silico Phage Hunting: Bioinformatics Exercises to Identify and Explore Bacteriophage Genomes. |
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| المؤلفون: | Martinez-Vaz BM; Department of Biology, Hamline University, St. Paul, MN, United States., Mickelson MM; Department of Biology, Hamline University, St. Paul, MN, United States. |
| المصدر: | Frontiers in microbiology [Front Microbiol] 2020 Sep 17; Vol. 11, pp. 577634. Date of Electronic Publication: 2020 Sep 17 (Print Publication: 2020). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101548977 Publication Model: eCollection Cited Medium: Print ISSN: 1664-302X (Print) Linking ISSN: 1664302X NLM ISO Abbreviation: Front Microbiol Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Lausanne : Frontiers Research Foundation |
| مستخلص: | Bioinformatics skills are increasingly relevant to research in most areas of the life sciences. The availability of genome sequences and large data sets provide unique opportunities to incorporate bioinformatics exercises into undergraduate microbiology courses. The goal of this project was to develop a teaching module to investigate the abundance and phylogenetic relationships amongst bacteriophages using a set of freely available bioinformatics tools. Computational identification and examination of bacteriophage genomes, followed by phylogenetic analyses, provides opportunities to incorporate core bioinformatics competencies in microbiology courses and enhance students' bioinformatics skills. The first activity consisted of using PHASTER (PHAge Search Tool Enhanced Release), a bioinformatics tool that identifies bacteriophage sequences within bacterial chromosomes. Further computational analyses were conducted to align bacteriophage proteins, genomes, and determine phylogenetic relationships amongst these viruses. This part of the project was carried out using the Clustal omega, MAFFT (Multiple Alignment using Fast Fourier Transform), and Interactive Tree of Life (iTOL) programs for sequence alignments and phylogenetic analyses. The laboratory activities were field tested in undergraduate directed research, and microbiology classes. The learning objectives were assessed by comparing the scores of pre and post-tests and grading final presentations. Post-tests were higher than pre-test scores at or below p = 0.002. The data suggest in silico phage hunting improves students' ability to search databases, interpret phylogenetic trees, and use bioinformatics tools to examine genome structure. This activity allows instructors to integrate key bioinformatic concepts in their curriculums and gives students the opportunity to participate in a research-directed learning environment in the classroom. (Copyright © 2020 Martinez-Vaz and Mickelson.) |
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| فهرسة مساهمة: | Keywords: bacteriophages; bioinformatics; experimental design (study designs); genomes; phylogenetic trees; research project |
| تواريخ الأحداث: | Date Created: 20201019 Latest Revision: 20201022 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC7533560 |
| DOI: | 10.3389/fmicb.2020.577634 |
| PMID: | 33072043 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1664-302X |
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| DOI: | 10.3389/fmicb.2020.577634 |