DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition.

ABSTRACT: Transposable elements (TEs) are selfish DNA sequences that multiply within host genomes. They are present in most species investigated so far at varying degrees of abundance and sequence diversity. The TE composition may not only vary between but also within species and could have important biological implications. Variation in prevalence among populations may for example indicate a recent TE invasion, whereas sequence variation could indicate the presence of hyperactive or inactive forms. Gaining unbiased estimates of TE composition is thus vital for understanding the evolutionary dynamics of transposons. To this end, we developed DeviaTE, a tool to analyse and visualize TE abundance using Illumina or Sanger sequencing reads. Our tool requires sequencing reads of one or more samples (tiss

SUBMITTER: Weilguny L 

PROVIDER: S-EPMC6791034 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature