Part (B): Total counts of each type of TFBS in the dataset and number of motifs found in randomly generated sequences of length 1000 bp, and average sum of the motifs found in shuffled sequences (each sequence shuffled 10 times).
The algorithm for sequence shuffling works as follows: two different mono-nucleotides of a sequence are randomly chosen and swapped.
To test this, we generated by sequence shuffling 100 randomized sets of sequences with the same nucleotide composition as the regions around high-probability and low-probability miRNA target sites, respectively.
Nystedt et al. suggested that the switch in function of T4SSs was mediated by duplication of the pilus component encoding genes and their diversification by combinatorial sequence shuffling within and among genomes [12].
Motif and sequence shuffling were also used to account for G + C content biases.
For instance, the assembly process may have merged multiple homeologs into a single sequence, shuffling SNPs among homeologs.
Here we assumed that the distribution of SSR pairs was independent of the sequence structure of the genomic sequences and hence sequence shuffling would not affect their distribution.
Frequent sequence shuffling, i.e., acquiring a piece of a nucleotide sequence from different viruses, may have had important impacts on the evolution of enteroviruses.
We thus decided to investigate to what degree such small duplications have contributed to the mosaic duplication patterns of SDs in 22q11.2 and sequence shuffling between LCR22 blocks.
In a preliminary step to further analyze the relationships between global specificity towards steroids and sequence shuffling, Figure 5(b) illustrates a low resolution map of amino acid sequences of discussed chimera as compared to parental sequences.
To rule out the effect of base composition bias on robustness, four types of reference sets for each real pre-miRNA are made using four different sequence shuffling methods: mononucleotide shuffling, dinucleotide shuffling and shuffling based on a zero and first order Markov model.
