Bioinformatics for DNA Sequence Analysis.pdf - Index of

218 Zaneveld et al.Table 10.1Compositional properties calculated by CodonExplorer. Arbitrary combinationsof these values may be plotted against one another using the ‘‘Custom scatter plot’’optionNameCAI* – the codonadaptation indexP 3 – The third positionGC contentP 3 /CAILengthEquation/referenceCAI ¼ CAI obs /CAI maxCAI obs ¼QLRSCU kCAI max ¼RSCU ij ¼(14, 43) ð1=LÞk¼1 ð1=LÞQLRSCU k maxk¼1x ijP1 nin i j¼1 x ijG 3 þ C 3P 3 ¼A 3 þ T 3 þ C 3 þ G 3P 3 /CAI (see equations for P 3 and CAI, above)Gene lengthHydrophobicity Predicted peptide hydrophobicity (44)Horizontal transfer index(HTI)Ribosomal HTIPrðF jCOD i Þ PrðCOD i ÞPr(COD i |F) = P 6m¼1 PrðF jCOD mÞ PrðCOD m ÞþPrðF jNONÞ PrðNONÞ(m = 1,2,3,4,5,6)The probability that a gene was produced by a Markov model matchingin-frame coding genes in a genome (rather than other frames of codinggenes or non-coding sequence). Genes with low HTIs and lowribosomal HTIs (see below) have been proposed as transferred (30)The posterior probability that a gene matches the model for in-frameribosomal proteins in a genome, rather than intergenic regionsseparating ribosomal genes or the non-coding frames of ribosomalproteins. Calculated as the HTI above, but using ribosomal proteins orintergenic regions separating ribosomal proteins to build the coding andnon-coding models (30)Putative alien A putatively alien gene identified using the scheme of Nakamura et al. (30)Amino acid frequenciesThe frequency of individual amino acids, or a group of amino acids within agene. Available options includeA,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y, (DþE), (K þ R þ H) ,and (L þ I þ V þ M)*The equation shown for CAI is the traditional equation (14); the other CAI options are variants of thismeasure that may be useful for specific analyses.figure is generated showing a histogram of the average values foreach random set (Fig. 10.9). The blue circle (dark grey here)represents the mean value of the chosen property for these randomsets. The red circle represents the average of the chosen property