A standalone version of IsoFinder for the computational prediction of isochores in genome sequences

TL;DR

This paper introduces standalone software tools, IsoFinder and IsoFinderWin, enabling researchers to predict isochores in genome sequences locally, facilitating batch processing without web server limitations.

Contribution

The authors developed and released two standalone programs for isochore prediction, expanding accessibility beyond web-based analysis.

Findings

Two standalone programs successfully predict isochores in genome sequences.

The tools support batch processing for large datasets.

They are compatible with Windows and Linux systems.

Abstract

Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a researcher may want to perform batch processing of many sequences simultaneously in its local machine, instead of analyzing them on one by one basis through the web. To this end, standalone versions are required. We report here the implementation of two standalone programs, able to predict isochores at the sequence level: 1) a command-line version (IsoFinder) for Windows and Linux systems; and 2) a user-friendly version (IsoFinderWin) running under Windows.