ASPic

ASPIC predicts gene structures by identifying splice sites through integrated multiple alignments of expressed sequence tags (ESTs) to genomic sequences to represent constitutive and alternative splicing.

Key Features:

• Multiple genome-EST alignment algorithm: Integrates all available transcript data in a combined multiple-alignment strategy rather than aligning ESTs independently, improving splice site identification.
• Optimization-based splice site prediction: Recasts splice site prediction as an optimization problem that minimizes the number of exons and splice site observations to identify the optimal multiple transcript alignment.
• Dynamic programming for intron boundary refinement: Uses dynamic programming to refine intron boundaries for precise delineation of gene structures.
• Ad hoc procedures for efficient alignment: Implements ad hoc procedures for computationally efficient transcript alignment that distinguish it from BLAST-like methods.
• Minimal set of non-mergeable transcript isoforms: Outputs a minimal set of non-mergeable transcript isoforms compatible with the detected splicing events.
• Integration with databases: Integrates with genomic databases including Ensembl and Unigene for data retrieval and upload.
• Performance and efficiency: Benchmarking reports improved detection of novel splicing isoforms, reduced over-predictions, and lower computation time on individual genes and EST clusters.

Scientific Applications:

• Splice site prediction: Accurate identification of splice sites to support gene structure elucidation.
• Alternative splicing analysis: Detection and characterization of alternative splicing events to explore transcript diversity.
• Gene structure annotation: Support for comprehensive annotation of exon–intron structures in genome projects and functional genomics studies.

Methodology:

Combines all available EST data for alignment against genomic sequences; performs a novel multiple-alignment algorithm; frames splice site prediction as an optimization problem and employs dynamic programming to refine intron boundaries; determines non-mergeable transcript isoforms compatible with detected splicing events.