Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA.
The most generally applicable procedure for obtaining estimates of the symmetrical, or strandnonspecific, directional mutation pressure (microD) on protein-coding DNA sequences is to determine the G+C content at synonymous codon sites (Psyn), and to divide Psyn by twice the arithmetic mean of the G+C content at synonymous codon sites of a large number of randomly generated, synonymously coding DNA sequences (Psyn). Unfortunately, the original procedure yields biased estimates of Psyn and microD and is computationally expensive. We here present a fast procedure for estimating unbiased microD values. The procedure employs direct calculation of Psyn (approximately Psyn) and two normalization procedures, one for Psyn < or = Psyn and another for Psyn > or = Psyn. The normalization removes a bias sometimes caused by codons specifying arginine, asparagine, isoleucine, and leucine. Consequently, comparison of protein-coding genes that are translated using different genetic codes is facilitated.
Jermiin
L S
LS
Foster
P G
PG
Graur
D
D
Lowe
R M
RM
Crozier
R H
RH
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics; D004748:Entamoeba histolytica / Q000235:genetics; D016829:Giardia lamblia / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016296:Mutagenesis / Q000235:genetics*; D011506:Proteins / Q000235:genetics*
D004272:DNA, Mitochondrial; D011506:Proteins