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We then compute the similarity between two motifs using a distance measure between their corresponding KFVs.
To investigate if most of our targets contain an octamer motif, we screened all the peak regions of 497 target genes for OCT4 motifs, using a peak-score of 0.5 and ranked them based on a significance score.
In the second step, informative k-mers are converted into more informative degenerate motifs using a greedy search procedure, in which sets of amino acids are tested at individual positions of the motif and changes that lead to more informative motifs are preserved.
We search for the original and the reversed motifs using a hamming threshold of 6.
Rhee et al. [ 35] identifed cell cycle-related regulatory motifs using a kernel canonical correlation analysis.
We searched these databases for the presence of the motifs using a series of regular expressions.
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A recurrent musical motif using a bowdlerised pop version of Beethoven's 7th strikes a typically jarring note – at once cheesy and disposable, yet still lingering and profound.
A gene, LeCBP encoding a protein containing a PHD zinc finger motif and a bipartite nuclear localization signal, was identified from tomato pistils by its binding ability to a specific DNA motif using a yeast one-hybrid system.
These results show, for the first time, the molecular mechanism for reduced immunogenicity for the buried-ligand architecture and feasibility of targeting with this motif using a physiological ligand receptor pair.
ChIP assays were carried out using the ChIP-IT Express EnzymActiveit (Active Motif) using a dounce homoginizer to lyse cells.
In a program called poladq, Tabaska and Zhang [ 8] included the DSE motif using a quadratic discriminant function.
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