ASePCR

ASePCR predicts amplicon sizes from primer pairs to reveal transcript isoform diversity and tissue-specific alternative splicing by simulating RT-PCR using transcript models identified by NCBI's reverse e-PCR and EST evidence.

Key Features:

• Emulation of RT-PCR: Simulates reverse transcription PCR (RT-PCR) to predict amplicon sizes from specified primer pairs across transcript models.
• Integration with transcript models: Utilizes transcript models identified by NCBI's reverse e-PCR and supports RefSeq, Ensembl, ECgene, and AceView annotations for human, mouse, rat, and chicken genomes.
• Tissue-specific analysis: Deduces tissue specificity of predicted PCR bands by analyzing EST (expressed sequence tag) sequences compatible with each transcript structure.
• Gel-like output presentation: Produces gel electrophoresis–style displays of predicted PCR bands across tissues, with each band representing a potential isoform.
• EST alignments and tissue annotations: Reports EST alignments and associated tissue annotations linked to predicted bands.
• Comparative analysis: Facilitates comparison of alternative splicing (AS) patterns in orthologous genes across species.

Scientific Applications:

• Studying alternative splicing: Predicts transcript isoforms to support investigation of alternative splicing contributions to protein diversity.
• Comparative genomics: Enables analysis of AS patterns across species to identify conserved and divergent splicing events.
• Disease research: Identifies tissue-specific transcript variants that may be implicated in disease processes.

Methodology:

Simulates RT-PCR to estimate amplicon sizes for primer pairs from transcript models identified by NCBI's reverse e-PCR and integrates EST alignments to assign tissue specificity, using RefSeq, Ensembl, ECgene, and AceView transcript annotations for human, mouse, rat, and chicken.