HALO - Precise transcript half-life determination in Java
Recent improvements in experimental technologies for metabolic tagging and isolation of newly transcribed RNA now allow combined measurements of de novo transcription and RNA decay at whole transcriptome level in a single experimental setting.
Thus, transcript half-lives can be determined with a so far unreached accuracy. As several studies have shown, such transcript half-lives provide important insights into the regulation of biological processes on a much more general level than individual measurements of differential gene expression. In this article, we present HALO, the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command line tools and a well-documented Java API. Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the user interfaces provided as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines.