Jspinad/te-ger-order

TE-GER — Order Classification

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

TE-GER order classification model: classifies Transposable Elements by order (DIRS, HELITRON, LINE, LTR, PLE, SINE, TIR) 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 order

Labels

• 0: Background
• 1: DIRS
• 2: HELITRON
• 3: LINE
• 4: LTR
• 5: PLE
• 6: SINE
• 7: TIR

Citation

Developed by Johan S. Piña — 2025