Alternative splicing of gene transcripts presents biologists with challenges that have largely been ignored to-date. Assays commonly used by researchers to explore biological processes including qRT-PCR, RNAi, expression microarrays, and peptide-based technologies target sequence fragments to quantify or silence gene expression. Alternate splicing may cause failures for these assays and complicates interpretation of resulting data particularly when correlation between platforms is attempted. For example, qRT-PCR may fail to validate expression microarray results if the PCR primers and microarray probes target different splice variants. The purpose of this project is to implement a suite of tools that assist biologists in quickly and easily identifying the impact of alternative splicing on commonly used laboratory techniques. It is hoped that these tools will lead to more effective use of these technologies and to more insightful interpretation of resulting data.