Given an expression that denotes a probability distribution, often we want a corresponding density function, to use in probabilistic inference. Fortunately, the task of finding a density has been automated. It turns out that we can derive a compositional procedure for finding a density, by equational reasoning about integrals, starting with the mathematical specification of what a density is. Moreover, the density found can be run as an estimation algorithm, as well as simplified as an exact formula to improve the estimate.

UNLABELLED: : MGEScan-long terminal repeat (LTR) and MGEScan-non-LTR are successfully used programs for identifying LTRs and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not supported by easy-to-use interfaces nor well suited for data visualization in general data formats. Here, we present MGEScan, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters. MGEScan and Galaxy empower researchers to identify transposable elements in a graphical user interface with ready-to-use workflows. MGEScan also visualizes the custom annotation tracks for mobile genetic elements in public genome browsers. A maximum speed-up of 3.26× is attained for execution time using concurrent processing and MPI on four virtual cores. MGEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-based web server, and on a virtual cluster on the Amazon cloud. AVAILABILITY AND IMPLEMENTATION: MGEScan tutorials and source code are available at http://mgescan.readthedocs.org/ CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.