Manually Curated Library of Transposable Elements (TEs) and TE Annotations for Drosophila amaguana

This data collection provides a manually curated library of transposable elements (TEs) for Drosophila amaguana, including consensus sequences, genome-wide TE annotations, and individual TE copy sequences. The library was built using de novo generated by EDTA (Extensive de novo TE Annotator) and RepeatModeler, curated with MCHelper, and further processed for genome annotation using RepeatMasker and OneCodeToFindThemAll. 

Below is a description of the included files:

• Dama_curated_TE_library.fasta: Contains 737 consensus TE sequences manually curated for D. amaguana. Sequence identifiers include classification and origin (e.g., new families or similarity to known elements). The identifier for each sequence in the FASTA file includes information about its classification:
  
  
  • For sequences corresponding to potentially new families: The identifier consists of a three-letter abbreviation for D. amaguana (Dama), followed by the new family identifier and the superfamily name, all separated by underscores. Example: Dama_NF_BELPAO_1.
  • For consensus sequences that show similarity to TE sequences previously reported in other species: The identifier includes the abbreviation Dama, followed by the superfamily name and an abbreviation for the species in which the TE was previously reported, all separated by underscores. Example: Dama_Helitron-1_DVir.
    
    
• Dama_TE_annotations.out: Genome-wide annotation file of TE insertions produced with RepeatMasker and post-processed using OneCodeToFindThemAll to merge fragmented elements.
• Dama_TE_copies.fasta: FASTA file containing the extracted sequences of all annotated TE copies from the D. amaguana genome.
• TEcopies_sequences.sh: Shell script used to extract TE copy sequences from the genome using the annotation coordinates.
• Dynamics_Dama.ipynb: Jupyter Notebook for the analysis of transposable element (TE) dynamics in D. amaguana.