EVR

EVR reconstructs three-dimensional chromosome structures in prokaryotes from 3C and Hi-C interaction data using the Error-Vector Resultant (EVR) algorithm.

Key Features:

• Error-Vector Resultant Algorithm: Applies the Error-Vector Resultant (EVR) algorithm to reconstruct three-dimensional chromosome structures from interaction frequency matrices.
• Interaction Matrix Processing: Accepts normalized or unnormalized interaction frequency matrices derived from chromosome conformation capture experiments.
• PDB Structure Output: Generates reconstructed chromosome structures in Protein Data Bank (PDB) format for structural analysis and visualization.
• Parallelized Computation: Implements parallel computation using Cython and OpenCL to utilize multi-core CPUs and GPUs.
• Prokaryotic Chromosome Modeling: Supports reconstruction of closed-loop chromosome structures characteristic of prokaryotic genomes.

Scientific Applications:

• Prokaryotic Chromosome Structure Reconstruction: Models three-dimensional genome architecture of bacterial chromosomes from 3C and Hi-C interaction data.
• Chromosome Organization Studies: Enables analysis of spatial genome organization in prokaryotes.
• 3C/Hi-C Data Interpretation: Converts chromosome interaction frequency matrices into structural genome models.

Methodology:

EVR processes normalized or unnormalized interaction frequency matrices from 3C or Hi-C experiments using the Error-Vector Resultant algorithm to reconstruct three-dimensional chromosome structures and outputs models in PDB format.