NanoMod

NanoMod detects DNA modifications from raw Nanopore long-read sequencing signals to identify natural and synthetic nucleotide modifications at single-base resolution for genomic and functional analyses.

Key Features:

• Direct Detection from Raw Signals: Analyzes raw Nanopore signal data to identify naturally occurring modifications such as methylations and synthetic modifications introduced to one or more of the four standard nucleotides.
• Paired-Sample Signal Intensity Extraction: Extracts signal intensities from paired DNA samples (modified and unmodified) for comparative analysis.
• Base Error Correction Using Reference Sequence: Performs base error correction using a reference sequence to reduce sequencing errors prior to modification calling.
• Comparison of Signal Distributions: Identifies modified bases by comparing the distribution of raw signals between the modified and unmodified sample sets.
• Neighborhood Effects Modeling: Accounts for neighborhood effects, i.e., influences of neighboring bases on signal characteristics, to refine detection accuracy.
• Single-Base Resolution: Reports modification calls at single-nucleotide resolution.
• Performance Evaluation: Evaluated on simulated datasets covering various modification types and neighborhood effect magnitudes and on an E. coli dataset with 5-methylcytosine (5mC), outperforming other methods.

Scientific Applications:

• Functional Genomics: Mapping the roles of modified nucleotides in large-scale functional genomics experiments.
• DNA Methylation Analysis: Studying methylation patterns including 5-methylcytosine (5mC) at single-base resolution.
• Synthetic Biology: Detecting synthetically introduced nucleotide modifications in experimental systems.
• DNA Damage Studies: Assessing effects of DNA damage that result in modified bases.

Methodology:

Collect raw Nanopore signal data, extract and compare signal intensities between modified and unmodified samples, perform base error correction using a reference sequence, and analyze neighborhood effects to detect modified bases.