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

Usha, Yadav; Dinesh, C Sharma

doi:10.22376/ijpbs/lpr.2021.11.5.l81-87

Cited by 6 publications

(6 citation statements)

References 36 publications

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“…The genomes of the selected viruses were divided into 1000 base pair regions to ensure the maximum identification of Mirror repeats as per the requirements of the bioinformatics approach (FPCB) utilized. The total no of Mirror repeat sequences in the case of selected viruses varies in no and is given below in HIV-2 [23]. The same case is also true in the plant & animal domain [24][25][26][27].…”

Section: Resultsmentioning

confidence: 99%

Identification of Mirror Repeats in Viral Genomes using FPCB Analysis

Yadav¹,

Kumari²,

Yadav³

et al. 2023

Preprint

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The majority of living domains consist of DNA as genetic material with the minor exception of viruses. The unique nature of every species determines by its unique pattern of genome or gene products. The genomic features become an evident example of evolutionary study also. Different types of repeat patterns are observed in genomes of living domains including human beings whose two third portion of the genome is repetitive. Among the varied type of repeat sequences Mirror Repeats (MR) play crucial roles at the genetic level in every species. The major focus of our research is on identification & to check the distribution of mirror repeat. For this, we employed a bioinformatics-based approach refer as FASTA PARALLEL COMPLEMENT BLAST (FPCB) to identify unique mirror repeat (MR) sequences in some selected viral genomes from three different categories (Animal, Plant & Human). The identified repeats vary in their length as well as found to be distributed throughout the selected viral genomes. The maximum no of MR were reported in the case of Dengue virus (229) & minimum is in the case of TMV (97). In the remaining selected viruses - HCV, HPV, HTLV-1, PVY, Rabies virus 178, 156, 175, 203 & 204 MR sequences were reported. These sequences can be utilized in many ways like in molecular diagnosis, drug delivery target as well as evolutionary study, etc. The present research also helps in the development of novel tools of bioinformatics to study mirror repeats and their functional perspective in the context of their occurrence in all domains.

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Section: Resultsmentioning

confidence: 99%

Identification of Mirror Repeats in Viral Genomes using FPCB Analysis

Yadav¹,

Kumari²,

Yadav³

et al. 2023

Preprint

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“…DNA tracks with mirror symmetries were reported in many eukaryotic species ranging from yeast to humans (24,25) , chloroplast genome of Nicotiana tabaccum plants (26)(27)(28) and recently in the deadly SARS-CoV-2 viral strain (29) . Our previous work has also reported the presence of mirror repeats in the flowering genes of Arabidopsis thaliana (30) and in the genome of HIV (31) . This was huge in terms of their ubiquitous presence across all eukaryotic kingdoms and their parasites also.…”

Section: Introductionmentioning

confidence: 78%

In Silico Analysis of Structural Photosynthetic Genes of Arabidopsis thaliana for Unique Mirror Repeats

Yadav¹,

Yadav²,

Sharma³

2022

IJST

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Objectives:The underlying work explores mirror sequences in the photosynthetic genes of Arabidopsis thaliana. At present, these sequences are standing at the forefront to be explored for their origin, distribution and function in plants. Methods: FPCB, a recently developed bioinformatics approach was utilized for identification of mirror sequences. It is a three step strategy based on pattern matching of alignments, produced after aligning gene sequence and its complement using mega-BLAST. This algorithm was quick and efficient enough to characterize a range of mirror sequences. Findings: All the analyzed genes were reported to harbor great variety of mirror sequences at quite high frequencies. LHCA1 gene have the highest total count of these sequences and ATPB gene have lowest of all. A total of 401 unique mirror sequences of different lengths and compositions were reported in the twelve selected genes. Promoter motifs were found to be greatly enriched with these repeats. Eleven mirror sequences of significant lengths were also reported using the above approach. Novelty: This work is the very first attempt to characterize photosynthetic genes of Arabidopsis thaliana for mirror repeats. This will further aggravate efforts to develop fingerprinting techniques based on these unique mirror sequences, which are very powerful tools to study taxonomic and evolutionary relationships. Mirror sequences are also potential candidates as drug delivery systems and in molecular medicine.

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“…Similarly, Yadav et al reported 232 and 248 mirror repeats within HIV-1 and HIV-2 genome and also identified 61 mirror repeats within lacZ operon, 40 mirror repeats within trpE operon and 41 mirror repeats within araE gene of Escherichia coli strain K-12 substrain MF1655. Lang also reported imperfect mirror https://www.indjst.org/ repeats within gag gene of HIV-1 (40)(41)(42)(43) . These identified mirror repeats have any role in within the genome of C. elegans is still mysterious.…”

Section: Resultsmentioning

confidence: 99%

In silico Approach for the Identification of Mirror Repeats within ced-3 Gene of Caenorhabditis elegans

Dhankhar,

Yadav,

Bhardwaj

2024

IJST

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Objectives: The repetitive elements within the genome of eukaryotes form a significant portion and are associated with various molecular functions within a cell. The goal of our study is to determine a special type of repeat i.e., mirror repeat within complete ced-3 apoptotic gene and its exons. Methods: A simple computational approach was used to search mirror repeats within the eight exons and complete ced-3 gene of Caenorhabditis elegans (C. elegans). C. elegans is a model organism widely used to study genetics, and developmental biology and ced-3 is the main apoptotic gene responsible for cell death. Findings: We identified 140 mirror repeats within the different regions of the ced-3 gene of C. elegans. These identified mirror repeats are not restricted to the genome of C. elegans but are scattered among the genome of C. vulgaris, Xenopus tropicalis and Drosophila melanogaster. Novelty: This research work is the very first endeavor to characterize mirror repeats within the complete ced-3 gene and its exons. Nobody has been studied mirror repeats within ced-3 apoptotic gene of C. elegans. Mirror repeat has the potential to form triplex DNA and is also associated with several neurological disorders. Forthcoming studies will help us to explore the functions and nature of these identified mirror repeats. Keywords: Repetitive elements, mirror repeats, Caenorhabditis elegans and ced-3 gene

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

Cited by 6 publications

References 36 publications

Identification of Mirror Repeats in Viral Genomes using FPCB Analysis

Identification of Mirror Repeats in Viral Genomes using FPCB Analysis

In Silico Analysis of Structural Photosynthetic Genes of Arabidopsis thaliana for Unique Mirror Repeats

In silico Approach for the Identification of Mirror Repeats within ced-3 Gene of Caenorhabditis elegans

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