TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting.

ABSTRACT:

Motivation

Transposable elements (TEs) in eukaryotes often get inserted into one another, forming sequences that become a complex mixture of full-length elements and their fragments. The reconstruction of full-length elements and the order in which they have been inserted is important for genome and transposon evolution studies. However, the accumulation of mutations and genome rearrangements over evolutionary time makes this process error-prone and decreases the efficiency of software aiming to recover all nested full-length TEs.

Results

We created software that uses a greedy recursive algorithm to mine increasingly fragmented copies of full-length LTR retrotransposons in assembled genomes and other sequence data. The software called TE-greedy-nester considers not only sequ

SUBMITTER: Lexa M 

PROVIDER: S-EPMC7755421 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature