LtrDetector: A modern tool-suite for detecting long terminal repeat retrotransposons de-novo on the genomic scale

Abstract

AbstractLong terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and genomic evolution. 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 are concurrent or have features to support manual review of new elements. To overcome these limitations, we developed LtrDetector, which uses signal-processing techniques. LtrDetector is easy to install and use. It is not species specific. It utilizes multi-core processors available in personal computers. It is more sensitive than other tools by 14.4%–50.8% while maintaining a low false positive rate on six plant genomes.