Evidence map›Paper›PMID 35920776›Full record

ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2022

Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons.

Ruksana Aziz, Piyali Sen, Pratyush Kumar Beura, Saurav Das, Debapriya Tula, Madhusmita Dash, Nima Dondu Namsa, Ramesh Chandra Deka, Edward J Feil, Siddhartha Sankar Satapathy and 1 more

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Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.8field-weighted citation impact, top 31% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 10 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 4 institutions in 2 countries.

Ruksana AzizDepartment of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028 Assam, India.
Piyali SenDepartment of Computer Science and Engineering, Tezpur University, Tezpur, 784028 Assam, India.
Pratyush Kumar BeuraDepartment of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028 Assam, India.
Saurav DasDepartment of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028 Assam, India.
Debapriya TulaTCS Innovation, Tata Consultancy Services, Hyderabad, 500081 Telangana, India.
Madhusmita DashDepartment of Electronics and Communication Engineering, NIT, Papum Pare, 791113 Arunachal Pradesh, India.
Nima Dondu NamsaDepartment of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028 Assam, India.
Ramesh Chandra DekaCenter for Multidisciplinary Research, Tezpur University, Tezpur, 784028 Assam, India.
Edward J FeilDepartment of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK.
Siddhartha Sankar SatapathyDepartment of Computer Science and Engineering, Tezpur University, Tezpur, 784028 Assam, India.
Suvendra Kumar RayDepartment of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028 Assam, India.
Tezpur University · INNational Institute of Technology Arunachal Pradesh · INTata Consultancy Services (India) · INUniversity of Bath · GB

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.

Indexed as

Escherichia coli ProteinsSelection, GeneticCodonCodon, NonsenseDeoxyribonuclease (Pyrimidine Dimer)Escherichia coliEvolution, MolecularModels, GeneticCodonCodon, NonsenseDeoxyribonuclease (Pyrimidine Dimer)Escherichia coli ProteinsNei protein, E colidN/dSpretermination codonsynonymous/non-synonymous sitestransitiontransversion

Identifiers

PMID35920776
PMCPMC9358017
OpenAlexW4289593841

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.