TEMP: a computational method for analyzing transposable element polymorphism in populations.

ABSTRACT: Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate

SUBMITTER: Zhuang J 

PROVIDER: S-EPMC4066757 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature