Publications by authors named "Ivan Vanat"
Article Synopsis
- Transposable elements (TEs) in eukaryotes can insert into each other, leading to a mix of full-length elements and fragments, complicating their reconstruction and study.
- A new software tool called TE-greedy-nester was developed using a greedy recursive algorithm to improve the recovery of fragmented full-length LTR retrotransposons in genomic data, showing higher accuracy than existing tools.
- The software is available for use at a specified online location and supplementary data can be found in Bioinformatics online.
Background: Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements.
Results: We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family ("autoinsertions").