Semi-automated genome annotation using epigenomic data and Segway

2016/10/17 by Eric G. Roberts, Mickaël Mendez, Coby Viner +7 · 1 voice · 1 citation
Biochemistry, Genetics and Molecular Biology · #Gene expression and cancer classification #Genomics and Chromatin Dynamics #Genomics and Phylogenetic Studies

paper · pdf · doi:10.1101/080382

openalex publication_date 2016/10/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22

Abstract

Biochemical techniques measure many individual properties of chromatin along the genome. These properties include DNA accessibility (measured by DNase-seq) and the presence of individual transcription factors and histone modifications (measured by ChIP-seq). Segway is software that transforms multiple datasets on chromatin properties into a single annotation of the genome that a biologist can more easily interpret. This protocol describes how to use Segway to annotate the genome, starting with reads from a ChIP-seq experiment. It includes pre-processing of data, training the Segway model, annotating the genome, assigning biological meanings to labels, and visualizing the annotation in a genome browser.

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