Journal
BIOMOLECULES
Volume 6, Issue 4, Pages -Publisher
MDPI
DOI: 10.3390/biom6040042
Keywords
RNA modifications; reverse transcription; reverse transcription (RT) signature; RNA sequencing (RNA-Seq); Next-Generation Sequencing (NGS); candidate screening; alignment viewer
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Funding
- DFG [SPP1784, MH3397/12-1, MH3397/14-1]
- ANR HTRNAMod [ANR-13-ISV8-0001]
- International PhD Programme (IPP) at the Institute of Molecular Biology (IMB) Mainz
- Boehringer Ingelheim Foundation
- Agence Nationale de la Recherche (ANR) [ANR-13-ISV8-0001] Funding Source: Agence Nationale de la Recherche (ANR)
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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.
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