Multivariate analysis of the tRNA sequence influence on codon pairing preference

<p><b>Copyright information:</b></p><p>Taken from "tRNA properties help shape codon pair preferences in open reading frames"</p><p>Nucleic Acids Research 2006;34(3):1015-1027.</p><p>Published online 9 Feb 2006</p><p>PMCID:PMC1363775.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> PLS analysis was used to identify nucleotides in P and A-site tRNAs that were good predictors of codon pair residual values. Representative data (data subset in which cP3 = G) from the analysis is presented, split between panels A and B for ease of interpretation. The weights plots (A and B) shown report the quantitative relationship between the predictor variables (tRNA nucleotides) and dependent variable (codon pair residual), plotted for the two components used to model the data. On these plots, tRNA and codon nucleotides plotted close to the residual value plot position (filled square) are typically those associated with over-represented codon pairs. Conversely, those at the opposite end of a line that bisects the plot origin and residual value point are typically those associated with under-represented codon pairs. () PLS weights plot showing P- and A-site codon nucleotides together with P-site tRNA nucleotides (filled triangles) plotted versus the codon pair residual value (filled square). () A-site tRNA nucleotides (filled triangles) plotted versus the codon pair residual value (filled square). Filled circle symbols represent key A-site tRNA nucleotide positions indicated by the PLS analysis to be significant predictors of the residual value across three bacterial species tested. Influential A-site tRNA nucleotide positions (filled circles) are labelled with the standard cloverleaf model nucleotide position, and the nucleotide identity. () A cloverleaf model of the basic tRNA structure, indicating those positions on the tRNA that were identified as good predictors of the codon pair residual value. Positions identified as important for residual prediction in , and are indicated by filled circles, those important in either two or just one of the three organisms, as 2/3 and 1/3 filled circles, respectively. Sector shadings indicate positions where >40% (black) o