Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach
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RESEARCH
Open Access
Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach Ludovica Liguori1,2, Maria Monticelli3, Mariateresa Allocca1,2, Maria Vittoria Cubellis3,4* and Bruno Hay Mele3,5 From 13th Bioinformatics and Computational Biology Conference - BBCC 2018 Naples, Italy. 19-21 November 2018
* Correspondence: [email protected] 3 Dipartimento di Biologia, Università Federico II, 80126 Naples, Italy 4 Biology and Evolution of Marine Organisms Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy Full list of author information is available at the end of the article
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. Keywords: Marine biotechnology, Graduate education, Computer-based learning
Background At present any biologists should capitalize on the resources, data and programs, that are available online to make their experimental plans more efficient and cost-effective [1, 2]. For this reason, it is desirable to train students using a problem-solving approach that integrates in silico work into a multidisciplinary experimental project(a © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permi
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