In-silico evaluation of ‘Mirror Repeats’ In HIV Genome

Abstract

The repetitive sequences played an important role in the characterization of both prokaryotic & eukaryotic organisms. Various different patterns of repetitive sequences have also been identified in organisms. Among all the repeat sequences. Mirror Repeats (MR`s) play an important role in various types of neurological disorders. These MR`s have also been reported for structure determination of genomes, triplex DNA formation & various other genome functions. We have followed a distinguished method referred to as FPCB (FASTA PARALLEL COMPLEMENT BLAST) for the identification of MR`s. The above said method used to identify MR’s in both types of HIV viruses (HIV-1 & HIV-2). Present investigation reported that MR’s are frequently distributed in all the regions of the genomes of both types. As a result, 232 & 248 total numbers of MR`s identified in both the HIV-1 & HIV-2 genome respectively. In addition, it was also revealed that the majority of the identified sequences are imperfect. The maximum length of MR`s in HIV-1 is of 47 nucleotides (NTD`s), however in case of HIV-2, it is of 49 nucleotides (NTD`s). Present investigation will be helpful for further development of a link between mirror repeats and host genome, which will be a new trend to block the viral integration as well as pathogenicity.