RT Journal Article
SR Electronic
T1 Modified dN/dS for accounting transition and transversion frequency difference and non-sense substitution in genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.01.22.477328
DO 10.1101/2022.01.22.477328
A1 Ruksana Aziz
A1 Piyali Sen
A1 Pratyush Kumar Beura
A1 Debashis Das
A1 Madhusmita Dash
A1 Nima Dondu Namsa
A1 Ramesh Chandra Deka
A1 Edward J Feil
A1 Siddhartha Sankar Satapathy
A1 Suvendra Kumar Ray
YR 2022
UL http://biorxiv.org/content/early/2022/01/23/2022.01.22.477328.abstract
AB The dN/dS value is estimated in homologous protein coding gene sequences between two closely related organisms for studying selection on the genes. In the usual method of calculation of synonymous (S) and non-synonymous (NS) sites in codons, the transition and transversion rates are considered same as well as no difference of pretermination codons from the other codons regarding NS substitutions is considered. In this study we are proposing a modification in the method by estimating the S and the NS sites in codons by considering difference between the transition and transversion rates and the NS substitutions leading to non-sense codons in pretermination codons. So, the dN/dS value calculated by our approach was higher than that calculated by the earlier method. The modified method was applied in estimating dN/dS in 29 homologous gene sequences of Escherichia coli and Salmonella enterica. Impact of codon degeneracy and pretermination codons on the dN/dS values estimated by our method were observed clearly. Our method of estimation that considers the above features is a realistic representation of dN/dS values in coding sequences.Competing Interest StatementThe authors have declared no competing interest.