Conference Paper

RepCalc: a Tool For Calculating Transposable Element Density within the Genome

2018 International Conference on Bioinformatics and Computational Biology
Tamer Aldwairi, Federico Hoffmann, Benjamin Elam, Andy D. Perkins


 Transposable elements (TEs) are mobile genetic elements that comprise a large portion of the genome of many eukaryotic organisms. They can transpose directly through the use of cut/paste mechanisms or indirectly copy/paste mechanisms. TE’s can sometimes induce a harmful effect through inserting themselves in a gene, rendering it non-functional. A number of tools have been developed with the goal of providing annotation information for the location of TEs within the genome. Our tool provides the researchers with ways to speed up the process of analyzing, comparing and summarizing the important information, in regards to the distribution of the densities for different families and subfamilies of TEs, whether across the whole genome or within specific regions of interest (ROI). Equipping researchers with such a tool is an imperative necessity to the research community. To demonstrate the usefulness of our tool we used Piwi-interacting RNA (piRNA) clusters as our ROI in which we calculate the densities for the different families/subfamilies of TEs. We observed that the densities of TEs varies and heavily depends on the location being analyzed, whether it is a piRNA cluster, a gene, or other parts of the genome. 

BICOB 2018

Las Vegas, NV, USA
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