DENSE

DENSE automates the identification of de novo emerged genes in eukaryotes through a two-step Nextflow pipeline combining phylostratigraphy and genome comparisons.

Key Features:

• Phylostratigraphy-based TRG detection: Detects taxonomically restricted genes as the first step toward identifying de novo emerged genes.
• Genome comparison and synteny filtering: Filters taxonomically restricted genes for de novo emerged genes through genome comparisons and synteny search.
• Flexible strategy and parameter combinations: Provides various strategy and parameter combinations enabling adaptation to specific configurations or user-defined strategies through a rational framework.
• Reference database: Compiles predictions for seven model organisms into a requestable database for reference de novo emerged gene lists.

Scientific Applications:

• De novo gene identification: Identifies de novo emerged genes originating from previously noncoding DNA regions in eukaryotic genomes.
• Cross-species evolutionary analysis: Enables thorough analysis across species with different evolutionary rates to reveal metrics for defining input datasets and identifying favorable conditions for de novo gene detection.
• Bias control in genome annotations: Provides metrics to control potential biases in genome annotations during de novo gene detection.

Methodology:

DENSE implements a two-step automated Nextflow pipeline: first, detection of taxonomically restricted genes through phylostratigraphy; second, filtering of taxonomically restricted genes for de novo emerged genes via genome comparisons and synteny search.