DANTE
Protein domains Galaxy CLI
Domain-based annotation of transposable elements using the REXdb protein database
Finds and classifies the conserved protein domains of transposable elements in nucleotide sequences, by similarity search against the REXdb protein database. The domains it reports are the starting point for the element-level pipelines, and on their own they show which lineages are present.
Output
- A GFF3 file of protein domain positions, with lineage classification
- A FASTA file of the translated domain sequences
- Filtered subsets by domain type or quality
How to cite
- Novák P., Hoštáková N., Neumann P., Macas J. (2024) DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes. NAR Genomics and Bioinformatics 6. doi:10.1093/nargab/lqae113
- Neumann P., Novák P., Hoštáková N., Macas J. (2019) Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10. doi:10.1186/s13100-018-0144-1