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sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine

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MicroRNA Detection and Target Identification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1580))

Abstract

High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20–250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require a Linux environment but computers, system administrators, and bioinformaticians suppose additional costs that often cannot be afforded by small to mid-sized groups or laboratories. Web servers are an alternative that can be used if the data is not subjected to privacy issues (what very often is an important issue with medical data). However, in any case they are less flexible than stand-alone programs limiting the number of workflows and analysis types that can be carried out.

We show in this protocol how virtual machines can be used to overcome those problems and limitations. sRNAtoolboxVM is a virtual machine that can be executed on all common operating systems through virtualization programs like VirtualBox or VMware, providing the user with a high number of preinstalled programs like sRNAbench for small RNA analysis without the need to maintain additional servers and/or operating systems.

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Author information

Authors and Affiliations

  1. Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain

    Cristina Gómez-Martín, Ricardo Lebrón, José L. Oliver & Michael Hackenberg

  2. Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, Granada, Spain

    Ricardo Lebrón, José L. Oliver & Michael Hackenberg

  3. Queen Mary University of London, Dawson Hall, Charterhouse Square, London, UK

    Antonio Rueda

Authors
  1. Cristina Gómez-Martín
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  2. Ricardo Lebrón
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  3. Antonio Rueda
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  4. José L. Oliver
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  5. Michael Hackenberg
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Corresponding author

Correspondence to Michael Hackenberg .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of East Anglia, Norwich, United Kingdom

    Tamas Dalmay

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Gómez-Martín, C., Lebrón, R., Rueda, A., Oliver, J.L., Hackenberg, M. (2017). sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine. In: Dalmay, T. (eds) MicroRNA Detection and Target Identification. Methods in Molecular Biology, vol 1580. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6866-4_12

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  • DOI: https://doi.org/10.1007/978-1-4939-6866-4_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6864-0

  • Online ISBN: 978-1-4939-6866-4

  • eBook Packages: Springer Protocols

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