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Lastly, we applied relative entropy to estimate the distance between the distribution of nucleotides at each neighbouring position and the background distribution (see Relative entropy below).
In total 139 cases (65%), had a neighbouring position at that site and thus confirmed the consistency of the identified BAC-clone on the second reference genome.
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These findings are supported by examples where the regulation of the LM mediated interaction has been shown to depend on the modifications at neighbouring positions or is thought to benefit from the binding versatility of disordered regions.
In addition, although the hidden Markov models are unsuited to encode mutual information and long-range dependencies, if the structural features of one position reduce the possible choices of amino acids at neighbouring positions, this will impact the probability distribution of individual states (i.e. aa positions) in the corresponding hidden states of the Markov model built by HMMER.
Those findings are supported by examples where the regulation of the linear motif mediated interaction has been shown to depend on the modifications (e.g. phosphorylation) at neighbouring positions or is thought to benefit from the binding versatility of disordered regions.
At the opposite side of the haem, Asp-168 and Arg-332 occupy neighbouring positions, suggesting a contribution to the haem reaction with H2O2.
In fact, the main difference between our spaced words and the commonly used contiguous words is that spaced-word matches at neighbouring positions are statistically less dependent on each other.
Of the pairs of concurrent tumours that were located separately from each other in the single patient and marked with a pair of numbers under the sample name, the pairs that are located in neighbouring positions in the dendrogram are marked with thin red frames; those in split positions are marked with pairs of closed or open black arrows.
In many species the RNA polymerase oscillates between two neighbouring positions on the DNA, with this back-and-forth motion which is powered by thermal energy being converted into forward movement of the enzyme along the DNA when a new NTP binds to the growing messenger RNA molecule.
The optimal gene size was determined as the largest gene that fulfilled the following standards: first, ≥2 identical tumour samples were located at neighbouring positions in the tree diagram of cluster analyses because these samples have more common CNAs during carcinogenesis than any other tumours [ 27]; second, each cluster's sample constitution becomes constant.
The reproducibility of genomic copy-number profiles was also assessed by confirming (1) neighbouring positions in clustering dendrograms of samples from identical tumours [ 27] after adding samples from deeply invasive parts of the corresponding tumours and (2) consistency in the sample constitution of each cluster during repeated clustering with varying gene sizes.
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