Abstract
<h2>Abstract</h2> Current ribonucleotide mapping software is customized for data generated using only one type of ribonucleotide sequencing technique. To standardize the analysis of ribonucleotide sequencing experiments, we developed the bioinformatics toolkit, Ribose-Map. Through a series of analytical modules, Ribose-Map transforms raw sequencing data into summary datasets and publication-ready visualizations of results, allowing researchers to locate the genomic coordinates of ribonucleotides to single-nucleotide resolution, study the nucleotide sequence context of ribonucleotides, explore their genome-wide distribution, and identify hotspots of ribonucleotide incorporation. Ribose-Map does not require background knowledge of ribonucleotide sequencing analysis and assumes only basic command-line skills. Ribose-Map is available at https://github.com/agombolay/ribose-map.
Highlights
Description of softwareRibonucleotides (rNMPs) are the most abundant type of noncanonical nucleotides present in genomic DNA and are known to wreak havoc on genome stability. rNMPs often become incorporated into genomic DNA during DNA replication and repair by DNA polymerases, but they are normally removed by the RNase-H2-mediated ribonucleotide excision repair pathway [1]
Current ribonucleotide mapping software is customized for data generated using only one type of ribonucleotide sequencing technique
Ribonucleotides are the most abundant type of noncanonical nucleotides present in genomic DNA and are known to wreak havoc on genome stability. rNMPs often become incorporated into genomic DNA during DNA replication and repair by DNA polymerases, but they are normally removed by the RNase-H2-mediated ribonucleotide excision repair pathway [1]
Summary
Ribonucleotides (rNMPs) are the most abundant type of noncanonical nucleotides present in genomic DNA and are known to wreak havoc on genome stability. rNMPs often become incorporated into genomic DNA during DNA replication and repair by DNA polymerases, but they are normally removed by the RNase-H2-mediated ribonucleotide excision repair pathway [1]. Based on the BAM (Binary Alignment Map) file generated from the Alignment module, the Coordinate Module outputs a BED (Browser Extensible Data) file of the single-nucleotide genomic coordinates of rNMPs. Once the rNMP coordinates have been obtained, the user can run the Composition, Sequence, Distribution, and Hotspot modules to explore potential biological signatures of rNMP incorporation. In addition to studying rNMPs, Ribose-Map can be used to study the biological signatures of any singlenucleotide genomic coordinates of interest (e.g., single-nucleotide polymorphisms) To perform such an analysis, the user should bypass the Alignment and Coordinate modules of Ribose-Map and directly input a browser extensible data (BED) file containing the genomic coordinates of interest into the Composition, Sequence, Distribution and/or Hotspot modules. The Ribose-Map bioinformatics toolkit has the potential to assess the accuracy of the currently available rNMP sequencing techniques for the first time and provide insight into the biological mechanisms that regulate the presence of rNMPs in DNA and the effects of rNMPs on genome stability, DNA metabolism, and disease
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