Mutagenesis by aflatoxin in M13 DNA: Base-substitution mechanisms and the origin of strand bias

1989 ◽  
Vol 217 (1) ◽  
pp. 20-25 ◽  
Author(s):  
Sudhir Sahasrabudhe ◽  
Kumar Sambamurti ◽  
M. Zafri Humayun
Keyword(s):  
Base Substitution ◽  
Strand Bias ◽  
Dna Base

Power of the likelihood ratio test for models of DNA base substitution

2011 ◽  
Vol 38 (12) ◽  
pp. 2723-2737 ◽  
Author(s):  
G. B. Cybis ◽  
S. R.C. Lopes ◽  
H. P. Pinheiro
Keyword(s):  
Likelihood Ratio ◽  
Likelihood Ratio Test ◽  
Base Substitution ◽  
Ratio Test ◽  
Dna Base

SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates

2014 ◽  
Vol 15 (4) ◽  
pp. 723-736 ◽  
Author(s):  
Anders Gonçalves da Silva ◽  
William Barendse ◽  
James W. Kijas ◽  
Wes C. Barris ◽  
Sean McWilliam ◽  
...  
Keyword(s):  
Base Substitution ◽  
Strand Bias ◽  
Snp Discovery ◽  
Conversion Rates

scholarly journals Similar States in Continuous-Time Markov Chains

2009 ◽  
Vol 46 (02) ◽  
pp. 497-506 ◽  
Author(s):  
V. B. Yap
Keyword(s):  
Markov Chains ◽  
Continuous Time ◽  
Transition Matrix ◽  
Base Substitution ◽  
Continuous Time Markov Chain ◽  
Rate Matrix ◽  
Dna Base ◽  
Substitution Models ◽  
Finite State ◽  
Finite State Space

In a homogeneous continuous-time Markov chain on a finite state space, two states that jump to every other state with the same rate are called similar. By partitioning states into similarity classes, the algebraic derivation of the transition matrix can be simplified, using hidden holding times and lumped Markov chains. When the rate matrix is reversible, the transition matrix is explicitly related in an intuitive way to that of the lumped chain. The theory provides a unified derivation for a whole range of useful DNA base substitution models, and a number of amino acid substitution models.

Indole in DNA: Comparison of a Nucleosidic with a Non-Nucleosidic DNA Base Substitution

2009 ◽  
Vol 2009 (3) ◽  
pp. 364-370 ◽  
Author(s):  
Janez Barbaric ◽  
Claudia Wanninger-Weiß ◽  
Hans-Achim Wagenknecht
Keyword(s):  
Base Substitution ◽  
Dna Base

scholarly journals Similar States in Continuous-Time Markov Chains

2009 ◽  
Vol 46 (2) ◽  
pp. 497-506 ◽  
Author(s):  
V. B. Yap
Keyword(s):  
Markov Chains ◽  
Continuous Time ◽  
Transition Matrix ◽  
Base Substitution ◽  
Continuous Time Markov Chain ◽  
Rate Matrix ◽  
Dna Base ◽  
Substitution Models ◽  
Finite State ◽  
Finite State Space

In a homogeneous continuous-time Markov chain on a finite state space, two states that jump to every other state with the same rate are called similar. By partitioning states into similarity classes, the algebraic derivation of the transition matrix can be simplified, using hidden holding times and lumped Markov chains. When the rate matrix is reversible, the transition matrix is explicitly related in an intuitive way to that of the lumped chain. The theory provides a unified derivation for a whole range of useful DNA base substitution models, and a number of amino acid substitution models.

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