Compensatory nature of Chargaff’s second parity rule

Rapoport, Alexandra E.; Trifonov, Edward N.

doi:10.1080/07391102.2012.736757

Cited by 27 publications

(24 citation statements)

References 45 publications

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“…The Parity Rule 2 (PR2) bias was calculated based on the values of A/U-bias 'A3 / (A3 + U3)' and G/C-bias 'G3 / (G3 + C3)', they were plotted as the ordinate and abscissa, respectively. The centre of the plot is the place where both coordinates are 0.5, as well as, A = U and G = C according to Chargaff's rule (PR2) (Rapoport and Trifonov, 2013).…”

Section: Pr2-bias Plot Analysismentioning

confidence: 99%

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

Khodary

Anwar

2020

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In the present study, we analyzed genome-wide codon usage patterns in 13 SARS-CoV-2 isolates from different geo-locations (countries) by utilizing different CUB measurements. Nucleotide and di-nucleotide compositions displayed bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Relative Synonymous Codon Usage (RSCU) analysis revealed 8 common putative preferred codons among all the 13 isolates.Interestingly, all of the latter codons are A/U-ended (U-ended: 7, A-ended: 1). Cluster analysis (based on RSCU values) was performed and showed comparable results to the phylogenetic analysis (based on their whole genome sequences) indicating that the CUB pattern may reflect the evolutionary relationship between the tested isolates. To investigate the force (mutation and/or selection) influencing the pattern of CUB in SARS-CoV-2 coding sequences, we employed the following; (i). Effective number of codons (ENc), (ii). ENc-GC3 plot, (iii). Neutrality plot, and (iv) Codon adaptation index (CAI). According to their results, natural selection and/or other factors (not investigated in this study) may be the dominant force driving SARS-CoV-2 CUB. It is also worth mentioning that, by using the most expressed genes in human lung tissues as a reference set, some viral genes such as Nucleocapsid phosphoprotein, ORF7a protein, and surface glycoprotein had high CAI values which may indicate for selection force acting on their codon usage, as they play important roles in viral assembly and may help viruses avoid the host immune system. The outcome of our study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 viruses, and the interactions with their host. Also, it may aid in vaccine design strategies.

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Section: Pr2-bias Plot Analysismentioning

confidence: 99%

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

Khodary

Anwar

2020

Preprint

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“…In this Section we will study hidden regularities in long sequences of single stranded DNA, which usually studied by some authors in relation with the second Chargaff's parity rule (see for example [Chargaff, 1971[Chargaff, , 1975Prahbu, 1993;Rapoport, Trifonov, 2012; https://en.wikipedia.org/wiki/Chargaff%27s_rules ]. The term "long DNA sequences" means that each of sequences contains no less than 100000 nucleotides.…”

Section: On Unitary Genetic Matrices and The Law Of Frequencies Of Hymentioning

confidence: 99%

The Genetic Coding System and Unitary Matrices

Petoukhov¹

2018

Preprint

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Information molecules of DNA and RNA should obey principles of quantum mechanics where unitary operators in form of unitary matrices have key meanings. Unitary matrices are the basis of calculations in quantum computers. This article presents some author's results, which show that matrix forms of the representation of structured systems of molecular-genetic alphabets can be considered as sets of sparse unitary matrices related with phenomenologic features of the degeneracy of the genetic code. These sparse unitary matrices have orthogonal systems of functions in their rows and columns. A complementarity exists among some unitary genetic matrices in relation each other.  Decompositions of numeric genetic matrices into sets of sparse unitary matrices are connected with the logical operation of modulo-2 addition used in quantum computers as well. Tensor (or Kronecker)  families of unitary genetic matrices with their fractal-like properties are also considered. The described results are discussed in the frame of development of quantum-information approaches for modeling genetic systems.

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“…In particular, symmetric deviations from k-mers frequence parity will have no effect on symmetrized signature. Indeed, it is known that Chargaff's second parity rule, stating that complementary nucleotides have the same frequency along a strand, may not hold for sequences shorter than a species-dependent "critical fragment length"; this length is comprised between 6 kbp and 50 kbp [51]. The parity rule seems the result of alternating regions with different signs of deviation from parity.…”

Section: Gcspr-based Signatures Have Better Error-tolerancementioning

confidence: 99%

The importance of Chargaff’s second parity rule for genomic signatures in metagenomics

Gori

Mavroeidis

Jetten

et al. 2017

Preprint

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An important problem in metagenomic data analysis is to identify the source organism, or at least taxon, of each sequence. Most methods tackle this problem in two steps by using an alignment-free approach: first the DNA sequences are represented as points of a real n-dimensional space via a mapping function then either clustering or classification algorithms are applied. Those mapping functions require to be genomic signatures: the dissimilarity between the mapped points must reflect the degree of phylogenetic similarity of the source species. Designing good signatures for metagenomics can be challenging due to the special characteristics of metagenomic sequences; most of the existing signatures were not designed accordingly and they were tested only on error-free sequences sampled from a few dozens of species.In this work we analyze comparatively the goodness of existing and novel signatures based on tetranucleotide frequencies via statistical models and computational experiments; we also study how they are affected by the generalized Chargaff's second parity rule (GCSPR), which states that in a given sequence longer than 50kbp, inverse oligonucleotides are approximately equally frequent. We analyze 38 million sequences of 150 bp-1,000 bp with 1% base-calling error, sampled from 1,284 microbes. Our models indicate that GCSPR reduces strand-dependence of signatures, that is, their values are less affected by the source strand; GCSPR is further exploited by some signatures to reduce the intra-species dispersion. Two novel signatures stand out both in the models and in the experiments: the combination signature and the operation signature. The former achieves strand-independence without grouping oligonucleotides; this could be valuable for alignment-free sequence comparison methods when distinguishing inverse oligonucleotides matters. Operation signature sums the frequencies of reverse, complement, and inverse tetranucleotides; having 72 features it reduces the computational intensity of the analysis.

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Compensatory nature of Chargaff’s second parity rule

Cited by 27 publications

References 45 publications

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

The Genetic Coding System and Unitary Matrices

The importance of Chargaff’s second parity rule for genomic signatures in metagenomics

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