To test for differences in gene placement along the mutation gradient between normal and modified mitochondrial genomes, we first estimated the average mutation position for each gene in each species.
We used a modification of these formulas to estimate absolute mutation position, which is not standardized by genome size, for each mitochondrial gene for all genomes because our goals include comparing estimates of mutation position for a given gene across genomes of different sizes.
We do not standardize for total genome size, as done in previous studies on mitochondrial mutational gradients (Tanaka and Ozawa 1994; Faith and Pollock 2003; Krishnan et al. 2004), because our goals include comparing estimates of mutation position for a given gene across genomes of different sizes.
Please note that for the mutation position of SNPs, different databases use different coordinate.
Several mutation positions have been chosen for introducing positively charged lysines in human cytochrome c (cyt c) with the aim of increasing the reaction rate with superoxide radicals (SO) and thus, the sensitivity of an electrochemical cyt c based SO biosensor.
Taking a user-defined parameter µ (number of novel mutations per gamete), GEMA creates mutations in the genomic sequences using random number generator for choosing mutation positions.
To assess the significance of observed intermolecular short distance enrichment for correlated mutation positions, we applied a randomization procedure where the original pairs of sequences that formed an input set for CAPS were randomly shuffled.
Finally, to assess the statistical significance of the observed preferred sequence-distance for correlated mutation positions within helices in the K-domain, we analyzed whether similar preferred sequence-distances occurred within randomly generated stretches of the sequence.
Analysis of the number of ortholog pairs in which a given motif pair had such consistent overlap with correlated mutation positions indicates that this is higher for the interacting pairs than for the non-interacting pairs (data not shown).
