RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing.

ABSTRACT:

Background

Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools.

Methods

We have developed the tool Relo

SUBMITTER: Chen J 

PROVIDER: S-EPMC5274521 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature