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Lack of functional enrichment for some of the modules may be attributed to the false discovery of the algorithm, the incompleteness of the GO annotations, or the non-functional relationship among genes in a module (e.g. genomic proximity).
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In these tests, the motif discovery phase of the algorithm was removed and the set of candidate models constructed as if the motif discovery algorithm had performed as well as possible at each candidate width.
MCOIN was initially evaluated without the motif discovery phase of the algorithm.
Subsequent evaluations use models computationally discovered by a MEME-based algorithm; the motif discovery phase of the algorithm is run as it would normally.
We note that the results for predictions at the known width are generally lower than when the motif discovery phase of the algorithm was removed.
Tests which removed the motif discovery phase of the algorithm showed that the mean information content per column ratio alone was sufficient to choose the true motif width.
Further, the results of experiments which removed the motif discovery phase of the algorithm show that, as the performance of this phase improves, the performance of MCOIN as a predictor of motif width also improves: as the discovered model becomes stronger and better models the true motif, the error in the width estimated by MCOIN will decrease.
The graphical interpretation of the χ2 statistic that we present in the paper is instrumental in our discovery of the efficient algorithm for finding the Hamming distance score.
More than a decade has passed since the discovery of the first quantum algorithm, but so far little progress has been made with respect to the "Holy Grail" of solving an NP-complete problem with a quantum-circuit model.
In 1755 the 19-year-old Lagrange wrote to Euler to announce the discovery of a new algorithm in the calculus of variations, a subject to which Euler had devoted an important treatise 11 years earlier.
Notwithstanding the excitement around the discovery of Shor's algorithm, and apart from the almost insurmountable problem of practically realizing and implementing a large scale quantum computer, a crucial theoretical question remains open, namely, what physical resources are responsible for the putative power of quantum computing?
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