Comprehensive analysis of repetitive extragenic palindrome sequences identified in bacteria and archaea using a new web-based tool, RepRanger.

ABSTRACT: Repetitive extragenic palindromic (REP) sequences were first discovered in the intergenic regions of Escherichia coli and later found in phylogenetically distinct bacterial species. However, their biological roles and sequence conservation remain unclear. Considering the growing number of microbial genome sequencing and annotation projects, along with the lack of online tools for REP identification, we developed a new web-based platform, RepRanger, to rapidly identify and annotate putative palindromic elements, including REPs. Using RepRanger, we identified >4,000 REPs in the E. coli MG1655 genome. Moreover, 81 (~52%) of its 157 small noncoding RNAs (sRNAs; known to regulate gene expression) contain REPs. Further analysis using RepRanger, alongside other bioinformatics tools,

SUBMITTER: Murashko ON 

PROVIDER: S-EPMC12306157 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature