Bioinformatical Approaches for Studies on Replication-Associated and Transcription-Associated Mutational Pressure, Interpretations and Applications, pp. 1-108
Authors: (Vladislav Victorovich Khrustalev, Eugene Victorovich Barkovsky, Belarussian State Medical University, Department of General Chemistry, Minsk, Belarus)
Abstract: This chapter describes bioinformatical approaches (including methods and descriptions of original computer algorithms) for studies on asymmetric mutational pressure. There are two types of asymmetric mutational pressure: replication-associated mutational pressure and transcription-associated mutational pressure. Our approaches help to study the effects of these two biological processes separately. Moreover, the methods described provide an opportunity to study nucleotide usage biases caused mostly by transitions separately from those caused mostly by transversions. Another bioinformatical method helps to distinguish nucleotide usage biases caused by transcription-associated mutational pressure from the bias occurred due to asymmetric negative selection on the fixation of amino acid substitutions. Thirty completely sequenced bacterial genomes, thirty six completely sequenced archaeal genomes and twelve completely sequenced genomes of alphaherpesviruses have been used as a factual
material for this chapter. Modifications of our bioinformatical methods for genomes with heterogenic GC-content distribution have been provided. Current knowledge on molecular mechanisms of nucleotide mutations occurrence and pathways of their reparation has been used during interpretations of the results obtained. These results can be used in studies on the estimation of the risk of non-synonymous and nonsense mutation occurrence in genomes and certain genes. To provide an example of this kind of application, we estimated probabilities of nonsense and synonymous mutation occurrence
in genes coding for M-proteins of Streptococcus pyogenes.