Computational Tools for a Novel Transcriptional Profiling Method
Teemu Kivioja · Työväentutkimus Vuosikirja · 2004
In this thesis we provide computational tools for the planning of VTT-TRAC experiments. VTT-TRAC is a novel method for measuring expression levels of genes. Monitoring gene expression by measuring the amounts of transcribed mRNAs (transcriptional profiling) has become an important experimental method in molecular biology. This has been due to rapid advance in the high-throughput measurement technology. Methods like microarrays are capable of measuring thousands of expression levels in one experiment. However, new methods that are fast and reliable are still needed. In addition to scientific research, such methods have important applications for example in medical diagnostics and bioprocess control. High-throughput technologies require automatic tools for planning of experiments. In VTT-TRAC a special fragment of DNA called a probe has to be selected for each profiled gene. In addition, the method allows multiplexing i.e. profiling a large number of genes together as a group called a