SHIP identifies genomic safe harbors in eukaryotic organisms using genomic general feature annotation.

ABSTRACT: Integrating foreign genes into loci, allowing their transcription without affecting endogenous gene expression, is the desirable strategy in genomic engineering. However, these loci, known as genomic safe harbors (GSHs), have been mainly identified by empirical methods. Furthermore, the most prominent available GSHs are localized within regions of high gene density, raising concerns about unstable expression. As synthetic biology is moving towards investigating polygenic modules rather than single genes, there is an increasing demand for tools to identify GSHs systematically. To expand the GSH repertoire, we present SHIP, an algorithm designed to detect potential GSHs in eukaryotes. Using the chassis organism Saccharomyces cerevisiae, five GSHs were experimentally curated based on data fro

SUBMITTER: Leitao MC 

PROVIDER: S-EPMC11871141 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature