Mutational bias

In eukaryotes, the existence of compositional biases is unclear and most attempts to detect the replication origins from strand compositional asymmetry have been inconclusive. Several studies have failed to show compositional biases related to replication, and analysis of nucleotide substitutions in the region of the -globin replication origin in primates do not support the existence of mutational bias... 

P. Lopez, and H. Philippe, Composition strand asymmetries in prokaryotic genomes mutational bias and biased gene orientation. C. R. Acad. Sci. HI 324, 201-208 (2001). 

Within positions Transitions versus trans-versions rRNA), reflecting constraints on stem regions to maintain secondary structure through base pairing Emphasizes mutational bias Weighting of transition bias which is most evident in vertebrate mitochondrial DNA but apparent in other systems as well. The general rule is that transitions occur more frequently than transversions and, as such, deserve less weight than the latter... 

Within and across positions Refers to weighting for both positional effects and mutational bias. A large number of combinations are possible... 

The first one is that changes in nucleotide composition correspond to changes in amino acids and, in turn, to changes in the hydrophobicity and in the secondary structure of proteins. If changes only depended upon mutational bias, then one should accept the untenable viewpoint that the corresponding functional changes are selectively irrelevant. 

Smith N.G.C. and Eyre-Walker A. (2001) Synonymous codon bias is not caused by mutation bias in G-tC rich genes in humans. Mol.Biol.Evol. 18 982-986. 

A powerful and general technique to enhance sampling is the use of umbrella potentials, discussed in Section IV. In the context of alchemical free energy simulations, for example, umbrella potentials have been used both to bias the system toward an experimentally determined conformation [26] and to promote conformational transitions by reducing dihedral and van der Waals energy terms involving atoms near a mutation site [67]. 

Wagner, S.D., Milstein, C., Neuberger, M.S. (1995). Codon bias targets mutation. Nature 376, 732. 

---