DANTE and DANTE_LTR: computational pipelines implementing lineage-centered annotation of LTR-retrotransposons in plant genomes
Long terminal repeat (LTR) retrotransposons represent a predominant class of repetitive DNA elements in the genomes of most plant species. As the number of sequenced plant genomes is growing at an accelerating rate, there is a need for computational tools that enable efficient annotation and classification of LTR retrotransposons in plant genome assemblies. Here, we present DANTE, a computational pipeline for Domain-based ANnotation of Transposable Elements, that performs sensitive detection of these elements based on the sequences of their conserved protein domains. The identified protein domains are then used by the DANTE_LTR pipeline to annotate complete element sequences by searching for their structural features, such as long terminal repeats, in the adjacent genomic regions. Moreover, the utilization of domain sequences enables the classification of elements into phylogenetic lineages, offering a more granular annotation compared to conventional coarse classification methods bas