ASPic-GeneID

ASPic-GeneID predicts protein-coding gene structures and alternative transcript isoforms by integrating EST-derived intron evidence from ASPic with constrained exon-chaining in GeneID for genome annotation.

Key Features:

• Lightweight pipeline: Provides a first-pass gene prediction workflow suitable for newly sequenced genomes and large-scale projects.
• EST integration (ASPic): Uses expressed sequence tag (EST) alignments to generate transcript annotations and intron predictions that serve as empirical evidence.
• GeneID integration: Adapts GeneID to incorporate ASPic-derived intron annotations to constrain exon-chaining and improve gene model consistency.
• Alternative isoform detection: Detects alternative transcript isoforms based on EST-derived transcript annotations.
• Improved sensitivity and specificity: Combines empirical EST evidence with ab initio exon chaining to enhance both sensitivity and specificity of gene predictions.

Scientific Applications:

• New genome annotation: Generates initial gene predictions for annotation of newly sequenced genomes.
• Transcriptome complexity analysis: Identifies alternative isoforms to study transcript diversity and gene regulation.
• Validation and benchmarking: Has been applied to the entire Caenorhabditis elegans genome and 44 ENCODE human pilot regions for evaluation.

Methodology:

ASPic processes EST alignments to produce transcript annotations and intron predictions; GeneID is modified to incorporate those intron annotations to constrain exon-chaining and produce gene predictions.