A problem with genotype data not present in standard sequence matching is that the information content of positions varies widely, with a preponderance of rare sites with very little information, which would mean that the length of hash word would need to change depending on position in the sequence.
It is noteworthy that "core" positions of TFBS are also depleted of CpGs having positive SCC M/E as compared to "flanking" positions (low information content of a position within PWM, (see Methods), although the results are not significant due to the low number of such CpGs (Additional files 7 and 8).
Seqlogo graphs display stacked letters for the nucleotides (i.e., A, C, G, T) at each aligned position, with the size of each letter being proportional to its frequency in the sequences and with the total height of all letters on each position reflecting the information content of the position.
The conservation of TFBSs in DNA sequences could be measured by the information content (IC) of position weight matrices (PWMs) of TFBSs [ 27].
In each position, each residue is a letter whose height is proportional to its frequency per position multiplied by the information content of each position measured in bits [ 57].
For each data set, we lined up the sequences so that the dinucleotide of interest was present in the central position and then we calculated the GC content of each position across all 2,000 sequences.
In a step called regularization, we add pseudo-counts to the position-specific distributions of the PFM according to the information content of the position (Rahmann, 2003).
The information content of a position within a binding site has been shown to correlate with the importance of that position in the formation of the protein-DNA complex [ 28].
This method adds the frequencies of the bases at each position, scaled between 0 and 1 for the least to most frequent, and weighted by the information content of the position.
