Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach

• Main Authors: Ludovica Liguori, Maria Monticelli, Mariateresa Allocca, Maria Vittoria Cubellis, Bruno Hay Mele
• Format: Article
• Language: English
• Published: BMC 2020-08-01
• Series: BMC Bioinformatics
• Subjects: Marine biotechnology; Graduate education; Computer-based learning
• Online Access: http://link.springer.com/article/10.1186/s12859-020-03560-z

Abstract Background Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students. Results We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students’ answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools. Conclusion Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.