AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes.

ABSTRACT: Short interspersed nuclear elements (SINEs) are a widespread type of small transposable element (TE). With increasing evidence for their impact on gene function and genome evolution in plants, accurate genome-scale SINE annotation becomes a fundamental step for studying the regulatory roles of SINEs and their relationship with other components in the genomes. Despite the overall promising progress made in TE annotation, SINE annotation remains a major challenge. Unlike some other TEs, SINEs are short and heterogeneous, and they usually lack well-conserved sequence or structural features. Thus, current SINE annotation tools have either low sensitivity or high false discovery rates. Given the demand and challenges, we aimed to provide a more accurate and efficient SINE annotation tool for pl

SUBMITTER: Li Y 

PROVIDER: S-EPMC8825457 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature