Inverted and mirror repeats in model nucleotide sequences

Lillo, Fabrizio; Spanò, M.

doi:10.1103/physreve.76.041914

Cited by 3 publications

(4 citation statements)

References 35 publications

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“…The S. cerevisiae genome is significantly enriched in perfect inverted repeats relative to random. Figure 6 plots in semilog coordinates the number of perfect IRs as a function of copy length for the S. cerevisiae , R, and RA genomes, together with expected numbers calculated using a theoretical method presented elsewhere (Lillo and Spano 2007 ). At every copy length the perfect IR number is statistically significantly higher in the S. cerevisiae genome than in either the R or the RA genomes.…”

Section: Resultsmentioning

confidence: 99%

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The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

et al. 2010

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Although a variety of possible functions have been proposed for inverted repeat sequences (IRs), it is not known which of them might occur in vivo. We investigate this question by assessing the distributions and properties of IRs in the Saccharomyces cerevisiae (SC) genome. Using the IRFinder algorithm we detect 100,514 IRs having copy length greater than 6 bp and spacer length less than 77 bp. To assess statistical significance we also determine the IR distributions in two types of randomization of the S. cerevisiae genome. We find that the S. cerevisiae genome is significantly enriched in IRs relative to random. The S. cerevisiae IRs are significantly longer and contain fewer imperfections than those from the randomized genomes, suggesting that processes to lengthen and/or correct errors in IRs may be operative in vivo. The S. cerevisiae IRs are highly clustered in intergenic regions, while their occurrence in coding sequences is consistent with random. Clustering is stronger in the 3′ flanks of genes than in their 5′ flanks. However, the S. cerevisiae genome is not enriched in those IRs that would extrude cruciforms, suggesting that this is not a common event. Various explanations for these results are considered.Electronic supplementary materialThe online version of this article (doi:10.1007/s00294-010-0302-6) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…Other authors (Lillo et al 2002 ; Lillo and Spano 2007 ) have presented formulas to compute the expected number of perfect IRs as a function of copy length in a sequence. We verified these formulas and also used them for the same purpose.…”

Section: Methodsmentioning

confidence: 99%

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

et al. 2010

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“…They play an important role in the regulation of transcription and translation (Varshney et al, 2020). Even in bacteria, inverted repeats and their associated hairpin structure are frequently found as a part of the independent transcription terminal (Brazda et al, 2020;Lillo and Spanò, 2007). Direct repeats are the sequences that are repeated multiple times on the same strand of DNA in the same orientation (Mirkin, 2001).…”

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Identification of mirror repeats within the Maleless (MLE) gene of Drosophila melanogaster Meigen

Kavita

Namrata

Deepti

et al. 2023

ije

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DNA repeats present in prokaryotes and eukaryotes genomes that include simple tandem repeats, satellite DNA, or palindromic sequences are classified as inverted, direct, and mirror repeats (MRs). Out of these, MRs are not well studied in Drosophila melanogaster Meigen. In this study, manual bioinformatics approach was used to find MRs in D. melanogaster maleless (mle) gene. In this analysis, 123 MRs were found within the complete mle gene, while 78 MRs were found in the exonic region of the mle gene. MegaBLAST was performed to elucidate the presence of identified MRs across the genomes of D. melanogaster, D. nasuta Lamb and D. bipectinate Duda. These demonstrated the conserved characteristics of specific MRs in Drosophila genome and the evolutionary and functional significance of MRs in diverse genomes. This study establishes a link between the presence of MRs in mle gene of D. melanogaster and MRs in human genome.

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“…Hairpin structures have been investigated in quite different organims with a variety of methods. Examples of these studies can be found in Ref.s [5,6,7,8,9,10,11,12,13,14] In this paper we detect candidate RNA secondary structures which are characterized by a minimal value of the free energy of the strucure in the folded state. In a first investigation the free energy is estimated by using Mfold, which is a reference software for the estimation of the free energy of RNA secondary structures.…”

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Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

et al. 2008

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By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.

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Inverted and mirror repeats in model nucleotide sequences

Cited by 3 publications

References 35 publications

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

Identification of mirror repeats within the <i>Maleless</i> (<i>MLE</i>) gene of <i>Drosophila melanogaster</i> Meigen

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

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