DARTS

DARTS identifies and annotates long terminal repeat retrotransposons (LTR-RTs) and mines conserved protein domains to support lineage classification and structural and functional analysis.

Key Features:

• Enhanced sensitivity: Identifies LTR-RTs with higher sensitivity than LTRharvest.
• Protein-domain mining: Mines sequences based on conserved protein domains within retrotransposons.
• Structural annotation output: Produces structurally annotated nucleotide and amino acid sequences for downstream analysis.
• Lineage and domain composition reporting: Reports lineage classification and protein domain composition of identified LTR-RTs.
• Customizable pipeline: Configurable to mine and annotate other groups of protein-coding transposable elements beyond LTR-RTs.

Scientific Applications:

• Lineage classification: Enables lineage classification of LTR-RTs based on conserved domain composition.
• Comparative and phylogenetic analyses: Provides annotated nucleotide and amino acid sequences immediately usable for comparative and phylogenetic studies.
• Retrotransposon diversity and evolution: Facilitates analysis of the diversity and evolutionary history of retrotransposons in eukaryotic genomes, particularly plants.
• Mining protein-coding TEs: Supports targeted mining and annotation of other protein-coding transposable elements.

Methodology:

DARTS mines sequences using conserved protein domain searches and returns structurally annotated nucleotide and amino acid sequences; its sensitivity has been benchmarked against LTRharvest.