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Methods in Next Generation Sequencing

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sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments

Guillermo Barturen
  • Department of Genetics, University of Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
  • Bioinformatics Group, Biomedical Research Center (CIBM), PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain
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/ Antonio Rueda
  • Genomics and Bioinformatics Platform of Andalusia (GBPA), Edificio INSUR, Calle Albert Einstein, 41092-Sevilla, Spain
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/ Maarten Hamberg
  • Department of Genetics, University of Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
  • Bioinformatics Group, Biomedical Research Center (CIBM), PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain
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/ Angel Alganza
  • Department of Genetics, University of Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
  • Bioinformatics Group, Biomedical Research Center (CIBM), PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain
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/ Ricardo Lebron
  • Department of Genetics, University of Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
  • Bioinformatics Group, Biomedical Research Center (CIBM), PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain
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/ Michalis Kotsyfakis
  • Biology Centre, Academy of Sciences of Czech Republic, Branisovska 31, 37005 Budweis, Czech Republic
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/ Bu-Jun Shi
  • Australian Centre for Plant Functional Genomics, the University of Adelaide, South, Australia 5064, Australia
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/ Danijela Koppers-Lalic / Michael Hackenberg
  • Department of Genetics, University of Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
  • Bioinformatics Group, Biomedical Research Center (CIBM), PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain
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Published Online: 2014-09-30 | DOI: https://doi.org/10.2478/mngs-2014-0001


MicroRNAs and other small RNAs are known to play important functions in gene regulation. Over the last years, it became also apparent that many virus genomes encode microRNAs and that those strongly interact with the host transcriptome. Important functions include the evasion of the immune response and the regulation of the switch to lytic infection. Since the advent of deep sequencing protocols for small RNAs, expression profiles can be routinely determined. However, currently the tools developed for the data analysis of small RNA deep sequencing experiments are limited to the analysis of only one species at a time. In order to facilitate the analysis of experimental setups that include genetic material from several species, we developed sRNAbench. It maintains the main features implemented in its predecessor program, miRanalyzer, and includes new functionalities such as full isomiR support including statistical test on differential frequency, improved prediction of novel microRNAs, extended summary files and data visualization support. Both a standalone program and a webserver are available at: http://bioinfo5.ugr.es/sRNAbench/.

Keywords: microRNA; small RNA; isomiRs; expression profiling; multi-species experiment; webserver


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About the article

Received: 2014-05-26

Accepted: 2014-08-11

Published Online: 2014-09-30

Citation Information: Methods in Next Generation Sequencing, Volume 1, Issue 1, ISSN (Online) 2084-7173, DOI: https://doi.org/10.2478/mngs-2014-0001.

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© 2014 Guillermo Barturen, et al.,. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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