Plant-LncPipe

Plant-LncPipe identifies and classifies plant long non-coding RNAs (lncRNAs) by retraining CPAT, PLEK, and LncFinder on plant-specific datasets and integrating retrained models into an ensemble to improve plant lncRNA prediction.

Key Features:

• Model retraining: CPAT, PLEK, and LncFinder were retrained using plant-specific datasets to improve prediction on plant transcripts.
• Retrained models: LncFinder-plant and CPAT-plant were selected through evaluation as the most effective retrained models for plant lncRNA identification.
• Ensemble integration: Retrained models are integrated into an ensemble within Plant-LncPipe to ensure robust lncRNA prediction performance.
• Comparative benchmarking: Performance was evaluated against CPC2, CNCI, RNAplonc, and LncADeep, which were developed using human or animal data.
• Reads mapping: The pipeline includes reads mapping as a data processing step.
• Transcript assembly: The pipeline performs transcript assembly as part of the analysis workflow.
• lncRNA identification: The pipeline identifies candidate long non-coding RNAs from assembled transcripts.
• Classification and origin determination: The pipeline classifies lncRNAs and determines their origin.

Scientific Applications:

• Functional studies of chromatin remodeling: Identification of plant lncRNAs to investigate roles in chromatin remodeling.
• Post-transcriptional regulation research: Identification of lncRNAs to study post-transcriptional regulation mechanisms in plants.
• Epigenetic modification studies: Identification of lncRNAs to explore contributions to epigenetic modifications.
• Developmental biology: Investigation of plant growth, root development, and seed dormancy through plant lncRNA analysis.
• Plant-specific lncRNA discovery: Improving detection of plant-specific lncRNAs that are poorly captured by models trained on animal or human data.

Methodology:

CPAT, PLEK, and LncFinder were retrained on plant-specific datasets; models were evaluated against CPC2, CNCI, RNAplonc, and LncADeep, resulting in selection of LncFinder-plant and CPAT-plant and their integration into an ensemble; the pipeline performs reads mapping, transcript assembly, lncRNA identification, classification, and origin determination.