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.

生物信息学技能与生命科学大多数领域的研究越来越相关。基因组序列和大数据集的可用性为将生物信息学练习纳入本科微生物学课程提供了独特的机会。该项目的目标是开发一个教学模块，使用一组免费提供的生物信息学工具来研究噬菌体之间的丰度和系统发育关系。噬菌体基因组的计算识别和检查，以及随后的系统发育分析，为将核心生物信息学能力纳入微生物学课程并提高学生的生物信息学技能提供了机会。第一项活动包括使用 PHASTER（PHAge 搜索工具增强版），这是一种生物信息学工具，可识别细菌染色体内的噬菌体序列。进行了进一步的计算分析来比对噬菌体蛋白、基因组，并确定这些病毒之间的系统发育关系。该项目的这一部分是使用 Clustal omega、MAFFT（使用快速傅里叶变换的多重比对）和交互式生命树 (iTOL) 程序进行序列比对和系统发育分析。实验室活动在本科生指导研究和微生物学课程中进行了现场测试。通过比较前后测试的分数并对最终演示进行评分来评估学习目标。后测试分数高于前测试分数，p = 0.002 或以下。数据表明，计算机噬菌体狩猎提高了学生搜索数据库、解释系统发育树以及使用生物信息学工具检查基因组结构的能力。 这项活动使教师能够将关键的生物信息学概念融入到他们的课程中，并让学生有机会在课堂上参与研究导向的学习环境。