A large fraction of mammalian genomes consist of transposable
elements (TEs). These elements are segments of DNA that historically either
moved or were copied from one place in the genome to another.
This process is still ongoing.
TE movements can cause deleterious mutations and drive chromosome
evolution.
We have developed a tool called ELITE to detect TE insertions, both
new and known efficiently. Code for ELITE is available on
github.
Please cite ELITE as follows:
Kashfeen, A., Fauni, H.B., Bell, T.A., Pardo-Manuel de Villena, F. and McMillan, L., 2019, September.
ELITE: Efficiently Locating Insertions of Transposable Elements. In Proceedings of
the 10th ACM International Conference on Bioinformatics, Computational Biology and Health
Informatics
(pp. 183-189).
The following database of Transposable Elements in Mouse was created using ELITE.
This dataset includes primarily Endogenous Retrovirus TEs found in the Collaborative Cross
genetics reference population, and its eight founder mouse strains A/J, C57BL6/J, 129S1/SvImJ,
NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ.