Journal Article

HALO—a Java framework for precise transcript half-life determination

Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken and Ralf Zimmer

in Bioinformatics

Volume 26, issue 9, pages 1264-1266
Published in print May 2010 | ISSN: 1367-4803
Published online March 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq117
HALO—a Java framework for precise transcript half-life determination

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Summary: Recent improvements in experimental technologies now allow measurements of de novo transcription and/or RNA decay at whole transcriptome level and determination of precise transcript half-lives. Such transcript half-lives provide important insights into the regulation of biological processes and the relative contributions of RNA decay and de novo transcription to differential gene expression. In this article, we present HALO (Half-life Organizer), the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription or decay determined with microarrays or RNA-seq. 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 application programming interface (API). Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the provided user interfaces as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines.

Availability: Source code, executables and documentation are available at http://www.bio.ifi.lmu.de/software/halo

Contact: caroline.friedel@bio.ifi.lmu.de

Journal Article.  1731 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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