A New Repeat Family Detection Method Based on Sparse de Bruijn Graph

Abstract

Eukaryotic genomes are typically large and filled with both genes and multiple classes of repetitive DNA. The repetitive DNAs are a rapidly evolving genome component that can provide the raw material for novel selected functions and also indicate the mechanisms and history of genome evolution in any ancestral lineage. In order to facilitate a broader range of repeat analyses, we present a graph method for repeat family detection and characterization by using the sparse de Bruijn graphs. This program was written in JAVA and with numerous adjustable parameters. Testing of this program indicated that it can found all of the major repeats.