MoRSAIK: Sequence Motif Reactor Simulation, Analysis and Inference Kit in Python

TL;DR

MoRSAIK is a Python package designed for simulating, analyzing, and inferring RNA sequence motif dynamics in prebiotic chemistry, aiding research on the origins of life and RNA world hypotheses.

Contribution

It introduces a novel Python toolkit for efficient simulation and Bayesian inference of RNA motif reactions, addressing the exponential complexity of sequence space.

Findings

Enables simulation of RNA reactions up to four nucleotides long.

Allows inference of reaction parameters from experimental data.

Provides tools for analyzing and visualizing RNA motif dynamics.

Abstract

Origins of life research investigates how life could emerge from prebiotic chemistry only. One possible explanation provides the RNA world hypothesis. It states that life could emerge from RNA strands only, storing and transferring biological information, as well as catalyzing reactions as ribozymes. Before this state could have emerged, however, the prebiotic world was probably a purely chemical pool of short RNA strands with random sequences and without biological function performing hybridization and dehybridization, as well as ligation and cleavage. In this context relevant questions are what are the conditions that allow longer RNA strands to be built and how can information carrying in RNA sequence emerge? In order to investigate such RNA reactors, efficient simulations are needed because the space of possible RNA sequences increases exponentially with the length of the strands, as well as the number of reactions between two strands. In addition, simulations have to be compared to experimental data for validation and parameter calibration. Here, we present the MoRSAIK python package for sequence motif (or k-mer) reactor simulation, analysis and inference. It enables users to simulate RNA sequence motif dynamics in the mean field approximation as well as to infer the reaction parameters from data with Bayesian methods and to analyze results by computing observables and plotting. MoRSAIK simulates an RNA reactor by following the reactions and the concentrations of all strands inside up to a certain length (of four nucleotides by default). Longer strands are followed indirectly, by tracking the concentrations of their containing sequence motifs of that maximum length.