CoreDetector

CoreDetector performs alignment of core-genome sequences across evolutionarily diverse genomes to detect sequence and structural variations and to identify representative non-redundant core-genome sequences within populations.

Key Features:

• Core-genome alignment: Performs alignment of core-genome sequences across evolutionary diverse genomes.
• Eukaryotic whole-genome processing: Handles larger eukaryotic genomes and a wide range of genome sizes and divergence levels.
• Variation detection: Supports determination of sequence and structural variations from whole-genome alignments.
• Non-redundant core identification: Identifies representative non-redundant core-genome sequences within populations.
• Prokaryote-focused limitation handling: Addresses limitations of tools primarily tailored for prokaryotes when applied to eukaryotic genomes.
• Comparative performance: Exhibits enhanced flexibility, efficiency, and competitive accuracy compared to other multiple genome alignment tools.
• Validation datasets: Validated on datasets including closely related fungal pathogen genomes, hexaploid wheat cultivar genomes, and more divergent fly and rodent species genomes.
• Implementation: Implemented in Java.

Scientific Applications:

• Comparative genomics: Enables comparative genomics analyses across eukaryotic species by providing core-genome alignments.
• Evolutionary biology: Supports evolutionary biology studies by facilitating detection of sequence and structural variation and identification of conserved core regions.
• Population genetics: Aids population genetics through identification of representative non-redundant core-genome sequences within populations.
• Plant and crop genomics: Applicable to crop genomics analyses such as comparisons among hexaploid wheat cultivars.
• Pathogen genomics: Applied to comparative analyses of closely related fungal pathogen genomes.
• Genomic divergence studies: Suited for analyses of genomic divergence in flies and rodent species.

Methodology:

Performs whole-genome core-genome alignment and identification of representative non-redundant core-genome sequences; implemented in Java.