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.

HALO is freely available to all academic users

First steps

For all user interfaces the functions of HALO are described in the documentation on a step-by-step basis for an example use case (half-lives in mouse fibroblasts) [see use case documentation for GUI, commandline version and Java API]. The data for this use case can be downloaded together with the HALO distribution or separately (see Downloads).

Alternatively you can test the GUI (e.g. using the Java Webstart version available below) with an example session which automatically performs the most important steps with HALO. Simply download the session from the Download section and load it by choosing the Load session option from the Session menu in the top left of the GUI. All steps will then be performed automatically and you only need to decide whether to save plots and plotting information or not. Note: After loading the session, it may take a few moments until you see the result.

Thus, the easiest way to get familiar with HALO (after installing it or using the webstart version) is to follow this step-by-step introductions or load the example session.