spotter

spotter simulates transcription, translation, and DNA supercoiling in prokaryotes using a stochastic single-nucleotide-resolution model to connect mechanistic details with cellular-scale sequencing data.

Key Features:

• Integrated Simulation Model: Combines representations of transcription, translation, and DNA supercoiling into a unified stochastic framework.
• High-Resolution Output: Produces single-nucleotide-resolution outputs providing positional information on residues and enabling visualization of individual simulation trajectories.
• Data Integration: Incorporates nascent transcript and ribosomal profiling sequencing data to bridge single-molecule experiments and cellular-scale high-throughput sequencing.
• Comparative Output Generation: Generates outputs that can be aggregated and compared with next-generation sequencing and proteomics data.

Scientific Applications:

• Mechanistic Studies: Investigates the coordination of transcription and translation and their interplay with DNA supercoiling in prokaryotes at molecular detail.
• Data Validation and Hypothesis Generation: Validates and compares simulation trajectories with high-throughput sequencing and proteomics datasets to support hypothesis generation.

Methodology:

Implements a stochastic simulation at single-nucleotide resolution that integrates models of transcription, translation, and DNA supercoiling and incorporates nascent transcript and ribosomal profiling sequencing data; outputs individual simulation trajectories for aggregation and comparison with next-generation sequencing and proteomics data.