ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes

Introduction

ORIS is a novel tool, written in JAVA, that lets the user interactively explore the whole genome sequence data using a number of computational methods and charts. ORIS is well suited for finding the origin of replication sites across bacteria, archaea and to some extent eukaryotes. ORIS successfully predicted the origin of replication sites in the genome of Plasmodium falciparum (Agarwal, M., Bhowmick, K., Shah, K., Krishnamachari, A., & Dhar, S. K. (2017). Identification and characterization of ARS‐like sequences as putative origin (s) of replication in human malaria parasite Plasmodium falciparum. The FEBS journal, 284(16), 2674-2695.).

ORIS is developed particularly for biologists and researchers who are working in the area of DNA replication. ORIS allows users with little or no programming background to interactively explore whole genome sequences and identify the putative origin of replication sites in the genome of interest. All the computational methods implemented in ORIS are accessible through a simple and intuitive GUI. We hope this will help biologists comprehensively analyze their DNA sequences. We have described applicability of our tool, ORIS, in a case study available as a supplementary document (https://github.com/urmi-21/ORIS). The method details could also be found in the supplementary document. A user guide is available from https://github.com/urmi-21/ORIS.

Getting Started

Prerequisites

• Java Runtime Environment 8 (or higher)

Downloading and Installing

ORIS is freely available to download from https://github.com/urmi-21/ORIS/releases. Download ORISv1.0.zip, and unzip the contents. In the unzipped folder find the ORISv1.0.jar file, this is the ORIS program. No further installation is required. DOUBLE CLICK on the .jar file icon to start ORIS.

User Guide

User guide describing the functionality is available at: https://github.com/urmi-21/ORIS/blob/master/OrisGuide.pdf

Methods and Case Study

A document describing ORIS' methods along with a case study is available here: https://github.com/urmi-21/ORIS/blob/master/ORIS_SI.pdf

Testing ORIS

Please see https://github.com/urmi-21/ORIS/tree/master/test

Building

For building instructions please see https://github.com/urmi-21/ORIS/blob/master/CONTRIBUTING.md

Citation

Please cite as: Singh et al., (2019). ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes. Journal of Open Source Software, 4(40), 1589, https://doi.org/10.21105/joss.01589

Examples

Reading Genome Data

Plotting GC-Skew

Searching Motifs

Developers

Urminder Singh

Java dependencies

• jmathplot

License

This project is licensed under the GNU GPL License - see the LICENSE file for details

Community Guidelines

Please report all the bugs through GitHub here. Please see CONTRIBUTING for guidelines on how to contribute to this project.