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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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Segmenting the Human Genome into Isochores.

Paolo Cozzi¹, Luciano Milanesi², Giorgio Bernardi³

¹National Research Council, Institute for Biomedical Technologies, Segrate, Milan, Italy. ; Parco Tecnologico Padano, Lodi, Italy.

Evolutionary Bioinformatics Online

|December 8, 2015

Summary

This study introduces isoSegmenter, a novel, fast, and automatic method for segmenting the human genome into isochores. This tool aids in understanding genome organization and long-range genomic features.

Keywords:

bioinformatics comparative genomics evolution

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

The human genome is organized into isochores, DNA sequences with homogeneous base composition.
Mammalian genome compartmentalization has been studied for decades, yet automatic isochore segmentation remains challenging.

Purpose of the Study:

To critically evaluate existing genome segmentation methods.
To introduce isoSegmenter, a novel, fast, and fully automatic approach for isochore segmentation.

Main Methods:

Developed isoSegmenter, an algorithm for genome segmentation into isochores.
Utilized experimentally defined parameters: compositional boundaries of isochore families and an optimal 100 kb window size.

Main Results:

isoSegmenter provides fast and automatic genome segmentation into isochores.
The method improves upon existing genome segmentation techniques.

Conclusions:

isoSegmenter is a significant advancement for analyzing long-range genomic features in sequenced and assembled genomes.
The tool is publicly available for researchers to study genome organization.