We apply Markov chain lumping techniques to aggregate codons from an empirical substitution matrix. The standard genetic code as well as higher order amino acid substitution groups are identified. Since the aggregates are derived from first principles they do not rely on system dependent assumptions made beforehand, e.g. regarding criteria on what should constitute an amino acid group. We there...

Markov-process models of codon substitution were implemented that account for features of DNA sequence evolution (such as transition/transversion bias and codon usage bias) as well as heterogeneity of amino acid substitution pattern over sites. The codon (amino acid) sites are assumed to come from several classes (such as secondary structure categories), among which the rate of amino acid subst...

Markov-process models of codon substitution were implemented that account for features of DNA sequence evolution (such as transition/transversion bias and codon usage bias) as well as heterogeneity of amino acid substitution pattern over sites. The codon (amino acid) sites are assumed to come from several classes (such as secondary structure categories), among which the rate of amino acid subst...

Escherichia coli heat-stable enterotoxin Ip (STIp), which is a typical extracellular toxin consisting of 18 amino acid residues, is synthesized as a precursor consisting of pre (amino acid residues 1 to 19), pro (amino acid residues 20 to 54), and mature (amino acid residues 55 to 72) regions. Though the pre region functions as a conventional leader peptide that guides the following region to c...

Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate model...

Recently, an interesting question has emerged in the evolutionary interpretation of sequence substitution data as evidence of amino acid selection pressure. Specifically, the Ka/Ks metric was designed to measure selection pressure on amino acid substitutions, assuming that the synonymous substitution rate Ks reflects the neutral nucleotide substitution rate. However, there is increasing evidenc...

Standard protein phylogenetic models use fixed rate matrices of amino acid interchange derived from analyses of large databases. Differences between the stationary amino acid frequencies of these rate matrices from those of a data set of interest are typically adjusted for by matrix multiplication that converts the empirical rate matrix to an exchangeability matrix which is then postmultiplied ...

background: cholera toxin b subunit (ctb) has been extensively considered as an immunogenic and adjuvant protein, but its yield of expression is not satisfactory in many studies. the aim of this study was to compare the expression of native and mutant recombinant ctb (rctb) in pqe vector. methods: ctxb fragment from vibrio cholerae o1 atcc14035 containing the substitution of mutant ctxb for ami...

In this issue of Blood, Pidala et al add a missing piece of information on the impact of amino acid substitutions (AASs) at specific peptide positions of class I antigens.