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Biomolecules 2016, 6(4), 42; doi:10.3390/biom6040042

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
Received: 29 August 2016 / Revised: 20 October 2016 / Accepted: 21 October 2016 / Published: 10 November 2016
(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)
View Full-Text   |   Download PDF [1122 KB, uploaded 10 November 2016]   |  

Abstract

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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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

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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