Ribose-Map

Ribose-Map analyzes ribonucleotide (rNMP) sequencing data to map ribonucleotides embedded in genomic DNA at single-nucleotide resolution. It supports multiple high-throughput techniques, including ribose-seq, emRiboSeq, RHII-HydEn-seq, Alk-HydEn-seq, and Pu-seq, to characterize rNMP incorporation by replicative DNA polymerases.

Key Features:

• Single-Nucleotide rNMP Mapping: Identifies genomic coordinates of embedded ribonucleotides at base-level resolution.
• Genome-wide Distribution Analysis: Detects incorporation hotspots and genome-wide distribution patterns of rNMPs.
• Sequence Context Characterization: Determines nucleotide sequence context surrounding mapped ribonucleotides.
• Cross-Protocol Compatibility: Processes datasets from ribose-seq, emRiboSeq, RHII-HydEn-seq, Alk-HydEn-seq, and Pu-seq.

Scientific Applications:

• Ribonucleotide Incorporation Studies: Enables investigation of rNMP distribution, incorporation signatures, and potential functional impacts in genomic DNA.

Methodology:

Ribose-Map processes sequencing reads to identify rNMP-specific signatures, assigns precise genomic coordinates, and performs quantitative analyses of distribution patterns and local sequence context across the genome.