Chacko, J. | bioRxiv Science

bioRxiv2024

RiboGraph: An interactive visualization system for ribosome profiling data at read length resolution

SummaryRibosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses. In this study, we introduce RiboGraph, a dedicated visualization tool designed to work with .ribo files, a specialized and efficient format for ribosome occupancy data. Unlike existing solutions that rely on large alignment files and time-consuming preprocessing steps, RiboGraph operates on a purpose designed compact file type and eliminates the need for data preprocessing. This efficiency allows for interactive, real-time visualization at ribosome-protected fragment length resolution. By providing an integrated toolset, RiboGraph empowers researchers to conduct comprehensive visual analysis of ribosome occupancy data. Availability and ImplementationSource code, step-by-step installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling/ribograph. On the same page, we provide test files and a step-by-step tutorial highlighting the key features of RiboGraph.

bioinformatics↗

bioRxiv2022

Clustering and finite size effects in a two-species exclusion process

We study the cluster size distribution of particles for a two-species exclusion process which involves totally asymmetric transport process of two oppositely directed species with stochastic directional switching of the species on a 1D lattice. As a function of Q - the ratio of the translation rate and directional switching rate of particles, in the limit of Q [->] 0, the probability distribution of the cluster size is an exponentially decaying function of cluster size m and is exactly similar to the cluster size distribution of a TASEP. For Q >> 1, the model can be mapped to persistent exclusion process (PEP) and the average cluster size, [<]m[>] {propto} Q1/2. We obtain an approximate expression for the average cluster size in this limit. For finite system size system of L lattice sites, for a particle number density{rho} , the probability distribution of cluster sizes exhibits a distinct peak which corresponds to the formation of a single cluster of size ms ={rho} L. However this peak vanishes in the thermodynamic limit L [->] {infty}. Interestingly, the probability of this largest size cluster, P(ms), exhibits scaling behaviour such that in terms of scaled variable Q1 {equiv} Q/L2{rho}(1 -{rho} ), data collapse is observed for the probability of this cluster. The statistical features related to clustering observed for this minimal model may also be relevant for understanding clustering characteristics in active particles systems in confined 1D geometry.

biophysics↗