TaF

TaF predicts and annotates gene structures in filamentous fungi using taxonomic profiling and homology-based evidence to support genome-wide functional, transcriptomic, and comparative analyses.

Key Features:

• Taxonomic Profiling: Employs large-scale taxonomic profiling to identify close relatives for genome queries and generate reliable hints for gene prediction.
• Exon-Intron Boundary Prediction: Uses orthologous protein sequence data from profiled species to produce extrinsic evidence of exon-intron boundaries, reducing false-positive predictions from distant orthologs.
• Hybrid Gene Prediction Methodology: Integrates ab initio and evidence-based prediction methods to improve gene model sensitivity and specificity for newly sequenced or uncharacterized fungal genomes.
• Homology Search Integration: Performs homology searches on predicted gene models to validate their biological relevance and accuracy.

Scientific Applications:

• Gene Prediction and Annotation: Generates high-quality gene structure predictions and annotations for filamentous fungal genomes.
• Trait-Associated Gene Identification: Identifies genes linked to specific traits through homology-informed prediction and annotation.
• Transcriptome Profiling: Provides accurate gene models required for transcriptomic analyses and expression studies.
• Comparative Genomics and Evolutionary Analysis: Enables comparative genomic and evolutionary analyses by producing consistent gene models across related fungal species.

Methodology:

Computational steps include large-scale taxonomic profiling to identify close relatives, extraction of orthologous protein sequences to generate extrinsic exon-intron evidence, integration of ab initio and evidence-based gene prediction, and homology searches on predicted gene models.