DANTE_TIR is a bioinformatics tool designed for the identification of DNA transposable elements containing Terminal Inverted Repeats (TIRs). This tool leverages prior annotations from DANTE, a separate software that identifies conserved protein domains, specifically transposases.

DANTE_TIR identifies DNA transposons with Terminal Inverted Repeats (TIRs) based on pre-existing annotations of conserved transposase domains provided by the DANTE tool. It extends the annotation workflow by extracting and assembling sequences flanking these conserved domains to discover potential TIR motifs through comparative analysis.

1. Domain Annotation Input:
   • Utilizes output from DANTE, which identifies conserved transposase protein domains in genomic sequences.
2. Sequence Extraction:
   • Extracts genomic sequences upstream and downstream from the identified transposase domains.
3. Contig Assembly:
   • Upstream and donwstream flankig sequences from each superfamily are assembled into contigs.
4. TIR Detection:
   • Analyzes assembled contigs to identify conserved sequences potentially representing TIR motifs.
   • Compares the 5' and 3' ends of contigs to confirm inverted repeat structures.
5. Target Site Duplication (TSD) Analysis:
   • Upon TIR confirmation, the tool examines flanking regions to identify potential Target Site Duplications (TSDs).
6. Iterative Refinement:
   • Confirmed TIR sequences are reused in subsequent rounds of detection to improve sensitivity.

Each DNA transposon superfamily is analyzed separately, with parameters optimized specifically for the characteristics of each superfamily. Detection sensitivity depends on the abundance of transposon elements within the genome. Low-copy superfamilies may be difficult to detect due to insufficient sequence conservation while sensitivity is maximized for superfamilies that are well-represented in the genome.

Using conda:

conda install -c conda-forge -c r -c bioconda -c petrnovak  dante_tir

dante_tir.py -g annotation.gff3 -f genome.fasta -o output_directory [-c number_of_CPUs]

• -g, --gff3: GFF3 file with DANTE annotation of conserved domains of transposases (required).
• -f, --fasta: FASTA file with genome assembly (required).
• -o, --output_dir: Output directory where TIR results will be stored (required).
• -c, --cpu: Number of CPUs to use (optional, default = 1).

Output directory will contain:

• DANTE_TIR_final.gff3: GFF3 file with TIR annotations. GFF3 file includes following attributes:
  • tir_seq5 and tir_seq3: 5' and 3' TIR sequences
  • tsd : target site duplication sequence
  • Classification: classification into superfamily
  • ID : unique ID of the element
• DANTE_TIR_final.fasta: Fasta file with complete elements
• DANTE_TIR_{superfamily}.fasta: Fasta file with complete elements for each superfamily
• TIR_classification_summary.txt : Number of TIRs detected in each superfamily

To summarize the results of DANTE_TIR, you can use the dante_tir_summary.R script. This script generates a summary HTML report of the annotations. Additionally, the DNA transposon sequences are clustered using mmseq2 program and library of representative sequences is generated.

dante_tir_summary.R -g DANTE_TIR_final.gff3 -f genome.fasta -o summary_output_directory

• -g, --gff: GFF3 file with DANTE_TIR annotations (required)
• -f, --fasta: FASTA file with genome assembly (required)
• -o, --output: Output directory for summary results (required)
• -t, --threads: Number of threads to use (optional, default = 1)
• -d, --debug: Save intermediate data for debugging (optional)
• -m, --min_cluster_size: Minimum cluster size to report representative elements (optional, default = 3)

Output directory will contain:

• report.html: HTML report with summary of TIR annotations
• {superfamily}_representative_elements.csv: Table with information about representative elements and respective clusters sizes (multiplicity)
• {superfamily}_representative_elements_all.fasta: Fasta file with all representative elements
• {superfamily}_representative_elements_min{min_cluster_size}.fasta: Fasta file with representative elements meeting a minimum cluster size threshold
• all_representative_elements_min{min_cluster_size}.fasta: Combined fasta file with all representative elements from all superfamilies meeting a minimum cluster size threshold

• DANTE (required for initial conserved domain annotation)

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