Jspinad/te-ger-superfamilies

TE-GER — Superfamily Classification

Part of the TE-GER (Transposable Elements Genomic Entity Recognition) toolkit.

TE-GER superfamily classification model: fine-grained TE annotation across 21 superfamilies (Gypsy, Copia, Mutator, HAT, etc.) in genomic sequences. Architecture: DNABERT-2 + BiLSTM hybrid.

Model Architecture

• Base: DNABERT-2 (DNA language model)
• Head: Bidirectional LSTM + Linear Classifier
• Input: 512 bp sliding windows over raw FASTA sequences
• Task: Sequence classification (token-level TE annotation)

Usage

Use this model via the TE-GER CLI:

python Te_annotator.py genome.fasta output.gff3 --level superfamilies

Labels

• 0: Background
• 1: ACADEM-1
• 2: BELPAO
• 3: CACTA
• 4: COPIA
• 5: CR1
• 6: DIRS
• 7: ERV
• 8: GYPSY
• 9: HAT
• 10: HELITRON
• 11: I
• 12: KOLOBOK
• 13: L1
• 14: LARD
• 15: LINE
• 16: LTR
• 17: MULE
• 18: P
• 19: PIFHARBINGER
• 20: PIGGYBAC
• 21: PLE
• 22: R1
• 23: RTE
• 24: SINE
• 25: TC1MARINER
• 26: TIR
• 27: TRNA

Citation

Developed by Johan S. Piña — 2025