ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing (AS) significantly increases transcript diversity in vertebrates.
• Reverse transcription-polymerase chain reaction (RT-PCR) is a key method for detecting AS variants.
• Understanding tissue-specific gene expression is crucial for biological research.

Purpose of the Study:

• To develop an efficient web-based application, ASePCR, for predicting tissue-specific transcript variants.
• To emulate RT-PCR to estimate amplicon sizes and visualize potential isoforms in various tissues.
• To provide a resource for exploring transcriptome diversity across different species and tissues.

Main Methods:

• ASePCR utilizes NCBI's reverse e-PCR program to identify transcript models.
• It estimates amplicon sizes for user-defined primer pairs.
• Tissue specificity is determined by analyzing expressed sequence tag (EST) compatibility with transcript structures.

Main Results:

• ASePCR generates an output simulating gel electrophoresis, displaying PCR bands representing putative tissue-specific isoforms.
• The tool provides EST alignment and tissue information within a genome browser.
• Users can compare alternative splicing patterns across orthologous genes in different species.

Conclusions:

• ASePCR serves as a valuable web resource for investigating transcriptome diversity.
• It facilitates the exploration of tissue-specific alternative splicing patterns.
• The application supports multiple transcriptome models and genomes, enhancing comparative analysis.