TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets.

ABSTRACT: Transposable elements (TEs) are non-static genomic units capable of moving indistinctly from one chromosomal location to another. Their insertion polymorphisms may cause beneficial mutations, such as the creation of new gene function, or deleterious in eukaryotes, e.g., different types of cancer in humans. A particular type of TE called LTR-retrotransposons comprises almost 8% of the human genome. Among LTR retrotransposons, human endogenous retroviruses (HERVs) bear structural and functional similarities to retroviruses. Several tools allow the detection of transposon insertion polymorphisms (TIPs) but fail to efficiently analyze large genomes or large datasets. Here, we developed a computational tool, named TIP_finder, able to detect mobile element insertions in very large genomes, throu

SUBMITTER: Orozco-Arias S 

PROVIDER: S-EPMC7563458 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature