scholarly journals Codon usage is a stochastic process across genetic codes of the kingdoms of life

2016 ◽  
Author(s):  
Bohdan B. Khomtchouk ◽  
Claes Wahlestedt ◽  
Wolfgang Nonner
Keyword(s):  
Amino Acids ◽  
Stochastic Process ◽  
Stochastic Model ◽  
Codon Usage ◽  
Random Variable ◽  
Mitochondrial Genomes ◽  
Genetic Codes ◽  
Protein Primary Structure ◽  
Truncated Normal ◽  
Codon Use

DNA encodes protein primary structure using 64 different codons to specify 20 different amino acids and a stop signal. To uncover rules of codon use, ranked codon frequencies have previously been analyzed in terms of empirical or statistical relations for a small number of genomes. These descriptions fail on most genomes reported in the Codon Usage Tabulated from GenBank (CUTG) database. Here we model codon usage as a random variable. This stochastic model provides accurate, one-parameter characterizations of 2210 nuclear and mitochondrial genomes represented with > 104 codons/genome in CUTG. We show that ranked codon frequencies are well characterized by a truncated normal (Gaussian) distribution. Most genomes use codons in a nearuniform manner. Lopsided usages are also widely distributed across genomes but less frequent. Our model provides a universal framework for investigating determinants of codon use.

The effect of expression levels on codon usage inPlasmodium falciparum

Parasitology ◽  
2004 ◽  
Vol 128 (3) ◽  
pp. 245-251 ◽  
Author(s):  
L. PEIXOTO ◽  
V. FERNÁNDEZ ◽  
H. MUSTO
Keyword(s):  
Amino Acids ◽  
Plasmodium Falciparum ◽  
Natural Selection ◽  
Codon Usage ◽  
Complete Sequence ◽  
Expression Data ◽  
Expression Levels ◽  
Synonymous Codons ◽  
Translational Selection ◽  
Highly Expressed Genes

The usage of alternative synonymous codons in the completely sequenced, extremely A+T-rich parasitePlasmodium falciparumwas studied. Confirming previous studies obtained with less than 3% of the total genes recently described, we found that A- and U-ending triplets predominate but translational selection increases the frequency of a subset of codons in highly expressed genes. However, some new results come from the analysis of the complete sequence. First, there is more variation in GC3 than previously described; second, the effect of natural selection acting at the level of translation has been analysed with real expression data at 4 different stages and third, we found that highly expressed proteins increment the frequency of energetically less expensive amino acids. The implications of these results are discussed.

Comparison of codon usage and tRNAs in mitochondrial genomes of Candida species

Biosystems ◽  
2007 ◽  
Vol 90 (2) ◽  
pp. 362-370 ◽  
Author(s):  
Takaaki Kamatani ◽  
Tetsuya Yamamoto
Keyword(s):  
Codon Usage ◽  
Candida Species ◽  
Mitochondrial Genomes

Analysis of synonymous codon usage patterns in different plant mitochondrial genomes

2008 ◽  
Vol 36 (8) ◽  
pp. 2039-2046 ◽  
Author(s):  
Meng Zhou ◽  
Xia Li
Keyword(s):  
Codon Usage ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mitochondrial Genomes ◽  
Usage Patterns

Peacocks and the Zeta distributions

2021 ◽  
Author(s):  
El ghazi Imad
Keyword(s):  
Stochastic Process ◽  
Random Variable ◽  
Short Paper ◽  
Convex Order ◽  
Increasing Process

Abstract We prove in this short paper that the stochastic process defined by: $$Y_{t} := \frac{X_{t+1}}{\mathbb{E}\left[ X_{t+1}\right]},\; t\geq a > 1,$$ is an increasing process for the convex order,where Χt a random variable taking values in N with probability P(Χt = n) = n-t/(𝛇(t)) and 𝛇(t) = +∞∑k=1(1/kt), ∀t > 1.

scholarly journals A Stochastic Model for Three Species

2018 ◽  
Vol 7 (4.10) ◽  
pp. 497
Author(s):  
Y. Suresh Kumar ◽  
N. Seshagiri Rao ◽  
B. V AppaRao
Keyword(s):  
Stochastic Process ◽  
Stochastic Model ◽  
Global Stability ◽  
Numerical Simulations ◽  
Local Stability ◽  
Equilibrium Points ◽  
Limited Resources

The present work is related to a three species ecosystem including a mutualism interaction between two species and a predator, where the predator is depending on both the mutual species. All three species in this model are considered in limited resources. The sustainability of the system (local stability) is discussed through the perturbed technique at the possible existing each equilibrium points. Using Lyapunov's technique the global stability of the system is also described. Further the nature of the system is observed by introducing the stochastic process to the species and the numerical simulations are studied to know the interaction among the species. 

Biologically Variable Respiration as a Stochastic Process in Ventilation – a Stochastic Model Study

2009 ◽  
pp. 53-55 ◽  
Author(s):  
Kyongyob Min ◽  
Keita Hosoi ◽  
Masayuki Degami ◽  
Yoshinori Kinoshita
Keyword(s):  
Stochastic Process ◽  
Stochastic Model ◽  
Model Study
Sign in / Sign up

Export Citation Format

Share Document