invertiaDB: a database of inverted repeats across organismal genomes

Nucleic Acids Res. 2025 Apr 22;53(8):gkaf329. doi: 10.1093/nar/gkaf329.

ABSTRACT

Inverted repeats are repetitive elements that can form hairpin and cruciform structures. They are linked to genomic instability; however, they also have various biological functions. Their distribution differs markedly across taxonomic groups in the tree of life, and they exhibit high polymorphism due to their inherent genomic instability. Advances in sequencing technologies and declined costs have enabled the generation of an ever-growing number of complete genomes for organisms across taxonomic groups in the tree of life. However, a comprehensive database encompassing inverted repeats across diverse organismal genomes has been lacking. We present invertiaDB, the first comprehensive database of inverted repeats spanning multiple taxa, featuring repeats identified in the genomes of 118 101 organisms across all major taxonomic groups. For each organism, we derived inverted repeats with arm lengths of at least 10 bp, spacer lengths up to 8 bp, and no mismatches in the arms. The database currently hosts 34 330 450 inverted repeat sequences, serving as a centralized, user-friendly repository to perform searches and interactive visualizations, and download existing inverted repeat data for independent analysis. invertiaDB is implemented as a web portal for browsing, analyzing, and downloading inverted repeat data. invertiaDB is publicly available at https://invertiadb.netlify.app/homepage.html.

PMID:40272360 | PMC:PMC12019632 | DOI:10.1093/nar/gkaf329