LoReAn

LoReAn integrates long-read complementary DNA (cDNA) sequencing, short-read cDNA sequencing, protein evidence, and ab initio prediction to annotate eukaryotic genomes and resolve complex transcript structures including alternative splice forms.

Key Features:

• Integration of Long-Read cDNA Sequencing: Leverages single-molecule full-length cDNA sequencing data from Pacific Biosciences and MinION to reveal intricate transcript structures and alternative splice forms.
• Comprehensive Data Utilization: Combines short- and long-read cDNA sequencing with protein evidence and ab initio prediction methods to produce comprehensive genome annotations.
• Enhanced Gene Prediction Accuracy: Demonstrated to outperform existing annotation pipelines by more accurately predicting gene structures and capturing genes missed by other tools.

Scientific Applications:

• Eukaryotic genome annotation: Produces improved gene models for eukaryotic genomes using integrated sequencing and evidence sources.
• Fungal genome annotation: Applied to annotate fungal genomes, including Verticillium dahliae and Plicaturopsis crispa.
• Plant genome annotation: Applied to annotate plant genomes, including Arabidopsis thaliana and Oryza sativa.
• Transcript structure and alternative splicing detection: Resolves intricate transcript structures and alternative splice forms from full-length cDNA reads.

Methodology:

Integrates short- and long-read cDNA sequencing data, incorporates protein evidence, and employs ab initio gene prediction algorithms.