REPrise: de novo interspersed repeat detection using inexact seeding.

ABSTRACT:

Background

Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-free de novo repeat detection approaches are powerful for annotating genomes that lack well-curated repeat databases. However, existing tools do not yet have sufficient repeat detection performance.

Results

In this study, we developed REPrise, a de novo interspersed repeat detection software program based on a seed-and-extension method. Although the algorithm of REPrise is similar to that of RepeatScout, which is currently the de facto standard tool, we incorporated three unique techniques into REPrise: inexact seeding, affine gap scoring and loose masking. Analyses of rice and simulation genome datasets showed

SUBMITTER: Takeda A 

PROVIDER: S-EPMC11966803 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature