The REG method is randomized by drawing from a skewed normal distribution based on the codon usage of the genome.
From the Plasmodium genome database, we collected 48,020 SNPs found within coding sequences and compared the distribution of their distance to the closest LCR to an expected distribution based on a random distribution of the SNPs in the genome.
The observed distribution was compared with the expected distribution based on 1,000 randomizations of the positions of the LCRs within the coding sequences of the reference genome taking into account the LCR size distribution.
Homologue species distribution based on BLASTx results.
Microsatellite information pertaining to the distribution based on motif-size, distribution in coding/non-coding regions, motif size-wise distribution and the density of repeats in coding regions of both the genomotif size-wiseratedistribution
In general, the nature and distribution of variations observed in this study follow the results on 1000 genomes data and expected distributions based on chromosome size (Figs. 3 and 4).
The observed distributions of TE-derived TFBS across classes/families, relative to their expected distributions based on the genome frequencies of the TE classes/families, are shown in Figure 1.
We evaluated the SNP distribution and genome coverage based on the whole genome sequence of M. truncatula[ 35], a close relative of alfalfa.
Consequently, alternative strategies such as genome classification based on gene distribution [ 5] and classification based on short nucleotide sequences [ 6] have recently been proposed to provide different perspectives for understanding their genomic relationships.
It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution.
Subsequently, we performed a statistical comparison of the functional distribution of genes affected by the SNPs and the overall functional distribution of all genes in the genome, based on the hypergeometric distribution.
