HiTE

HiTE employs a dynamic boundary adjustment approach for fast and accurate full-length transposable element detection and annotation.

Key Features:

• Dynamic boundary adjustment: HiTE detects full-length transposable elements with improved accuracy and robustness compared to existing methods.
• Novel transposon identification: HiTE identifies novel transposons with well-defined structures containing protein-coding domains, including some inserted within crucial genes leading to direct alterations in gene expression.
• Nextflow implementation: A Nextflow version provides enhanced parallelism, reproducibility, and portability.

Scientific Applications:

• Transposable element annotation: HiTE automates TE detection to supplement existing gold-standard TE databases that are not comprehensive even for extensively studied species.
• Comparative genomics: HiTE outperforms RepeatModeler2 across various species for genome-wide TE annotation using genome assemblies.
• Functional genomics: HiTE enables discovery of transposon insertions that directly alter gene expression through insertion within crucial genes.

Methodology:

HiTE uses a dynamic boundary adjustment approach for full-length transposable element detection and annotation.