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The gene parameters are set as follows: the population is 100, the iteration number is 500, the crossover probability is 0.9, and the mutation probability is 0.05.
Each promoter sequence includes 1 3 cis-regulatory elements, and an element that includes the gene parameters.
Average values of the above specified chromosome, sequence, and gene parameters were calculated using the data from the non-overlapping windows.
The analysis of gene parameters in the parasitoid wasp genome revealed a strong positive correlation between the recombination rate and gene content.
Next, we analyze chromosome, sequence, and gene parameters in the N. vitripennis genome and study their association with the recombination rate.
Even then, however, the accuracy of sequence and gene parameters that vary significantly within the genome might still differ between windows.
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An alternative method to evaluate parameter fit, is to compare the estimated parameters to the true gene parameter.
We then obtained significance values independently for each gene: parameter pairwise correlation by permuting the query gene/parameter 10,000 times and calculating the percent of permuted correlations that are more extreme (in either direction) than the non-permuted (observed) correlation.
To determine what combination of genes' parameters best predicts expression level, we performed multiple linear regression analyses.
To determine what combination of genes' parameters best predicts expression breadth, we performed multiple linear regression analyses.
Finally, total 10, 289 genes' parameters, including gene size, CDS length, first intron length, average intron length, and total intron length were estimated.
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