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Open AccessArticle

CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles

1
Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
2
Institute for Computer Sciences, Johannes Gutenberg University Mainz, Staudingerweg 9, 55128 Mainz, Germany
3
IMoPA UMR7365 CNRS-UL, BioPole de l’Université de Lorraine, 9 avenue de la Foret de Haye, 54505 Vandoeuvre-les-Nancy, France
*
Authors to whom correspondence should be addressed.
Academic Editor: Valérie de Crécy-Lagard
Biomolecules 2016, 6(4), 42; https://doi.org/10.3390/biom6040042
Received: 29 August 2016 / Revised: 20 October 2016 / Accepted: 21 October 2016 / Published: 10 November 2016
(This article belongs to the Collection RNA Modifications)
Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for the detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures of modified ribonucleotides relying on both sequence-dependent mismatch patterns and reverse transcription arrests. Common alignment viewers lack specialized functionality, such as filtering, tailored visualization, image export and differential analysis. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer (CAn) was developed in response to the demand for a powerful inspection tool. It is freely available for all three main operating systems. With SAM file format as standard input, CAn is an intuitive and user-friendly tool that is generally applicable to the large community of biomedical users, starting from simple visualization of RNA sequencing (RNA-Seq) data, up to sophisticated modification analysis with significance-based modification candidate calling. View Full-Text
Keywords: RNA modifications; reverse transcription; reverse transcription (RT) signature; RNA sequencing (RNA-Seq); Next-Generation Sequencing (NGS); candidate screening; alignment viewer RNA modifications; reverse transcription; reverse transcription (RT) signature; RNA sequencing (RNA-Seq); Next-Generation Sequencing (NGS); candidate screening; alignment viewer
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Hauenschild, R.; Werner, S.; Tserovski, L.; Hildebrandt, A.; Motorin, Y.; Helm, M. CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles. Biomolecules 2016, 6, 42.

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