LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo
Published in BMC Genomics, 2019
Recommended citation: Valencia, J.D., Girgis, H.Z. LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo. *BMC Genomics* **20**, 450 (2019). [](h ttps://doi.org/10.1186/s12864-019-5796-9) http://academicpages.github.io/files/LtrDetector.pdf
Long terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and defense mechanisms. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating long terminal repeat retrotransposons in these newly available genomes. However, the available tools are not very sensitive to known elements and perform inconsistently on different genomes. Some are hard to install or obsolete. They may struggle to process large plant genomes. None can be executed in parallel out of the box and very few have features to support visual review of new elements. To overcome these limitations, we developed LtrDetector, which uses techniques inspired by signal-processing.
Recommended citation: Valencia, J.D., Girgis, H.Z. LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo. BMC Genomics 20, 450 (2019). https://doi.org/10.1186/s12864-019-5796-9