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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.
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It has been noted that the hydrophobicity of a protein is related to the pyrimidine content of position 2 in the codons of the gene [ 11, 12].
Roughly, McTaggart's rationale for premise (2) is that the contents of positions are events.
Without the gap option, our algorithm attempts to maximize the total information content of all positions, which results in a motif with relatively uniform information content across all positions.
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).
Perhaps it is the radical content of the positions that is being ignored — and that has attracted public support, especially Mr. Paul's clear and consistent critique of the bloated military and "aid" budget.
If "socially conservative positions seem not just misguided but downright baffling," then, it might be because social conservatism's critics haven't taken the time to actually familiarize themselves with the actual content of those positions — preferring to tilt at caricatures instead.
The GC content of third positions (GC3) and coding regions (GCcds) exhibited significant correlations with the degree of codon bias.
The GC content of third positions and coding regions exhibited significant correlations with the magnitude of codon bias.
The ortholog data sets were analyzed with the program CodonW version 1.3 (Peden 1999) to estimate GC content of third positions for each synonymous codon (GC3).
We also evaluated if the information content of the positions within TFBS (measured for PWMs) affected the probability to find CpG "traffic lights" (Additional files 7 and 8).
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