RepeatExplorer

RepeatExplorer identifies and characterizes repetitive DNA elements in next-generation sequencing (NGS) datasets to determine repeat composition and evolutionary dynamics in plant and animal genomes.

Key Features:

• Graph-Based Clustering: Employs graph-based similarity clustering of short NGS reads to partition data into clusters representing individual repeat families.
• De Novo Identification: Performs de novo identification of repetitive elements without relying on reference databases of known elements.
• Repeat Annotation and Quantification: Provides programs for annotation and quantification of identified repeats, including classification of repeat types.
• Phylogenetic and Comparative Analyses: Supports investigation of phylogenetic relationships among retroelements and comparative analyses across multiple species.
• Visualization (SeqGrapheR): Includes visual inspection using SeqGrapheR to explore cluster structure and sequence variability.
• Scalability and Low-Pass Data Support: Scales to analyze low-pass genome sequencing and several million sequence reads to detect high- and medium-copy repeats.

Scientific Applications:

• Genome Structure and Evolution Studies: Enables characterization of repetitive sequence content to study genome structure and evolutionary dynamics in plants and animals.
• Repeat Family Analysis: Allows assessment of cluster sizes with statistical analyses and visual inspection to distinguish repeat types and intra-family sequence variability.
• Novel Element Discovery: Facilitates discovery and characterization of novel repeat elements and assembly of consensus sequences to investigate repeat family divergence.

Methodology:

Performs similarity-based graph partitioning of genome sequence reads into clusters representing repeat families; assembles consensus sequences; applies classification and quantification programs; uses statistical analysis of cluster sizes and visual inspection with SeqGrapheR; operates on low-pass NGS data and without reliance on reference repeat databases.