In silico approach for the identification of mirror repeats in selected operon genes of Escherichia coli strain K-12 substrain MG1655

Abstract

Background: The repeating elements in the genes or genomes of living organisms are associated with a variety of functions at the molecular level. Mirror repeats (MRs) are unique type of repeat sequences among them, which are found to be linked with H-DNA formation and they have also associated with several neurological disorders with many other functional roles are also being reported. Methods: The manual bioinformatics-based approach is used to identify the MRs in the genome. The applied approach FASTA-parallel complement-BLAST is used by following some simple steps to identify MRs. This methodology is initiated by the downloading of a sequence of interest in FASTA format followed by development of the parallel complement and final step of BLAST analysis. By using this approach, the present study identifies MRs in lac, trp, and ara operon genes of Escherichia coli str. K-12 substr. MG1655 (NC_000913.3). Results: Present investigation identified the frequent distribution MRs in all the analyzed operon genes. These identified MRs vary in their length or size. In case of lac, trp, and ara operon, maximum number of MRs reported in lacZ (61), trpE (40), and araE (41) genes, respectively. Conclusion: The frequent existence of MRs (shorter as well as larger length) in analyzed genes gives a hint about their significant roles in the genes or genomes of all bacterial species. These may be useful to study the evolutionary history of living world. These types of studies will be exploring new trends and tools of molecular biology research as well as development of new concept for MR identification.

Keywords

• blast
• fasta
• h-dna
• mirror repeats
• reverse complement