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This indicates a very narrow sequence window for TF-specific antibodies.
During DynaMine optimisation it was found that using a wider sequence window as an input for the predictor increases the correlation between DynaMine predictions and reference experimental data32.
Each sequence window is associated with a set of similar sequences from the genome (WPHs).
PCR primers were designed to amplify approximately 400 600 bp amplicons within a 1 Kb sequence window spanning the sequence represented by the associated microarray feature.
Primer selection was guided by uniqueness of the oligonucleotide sequence across the human genome, as well as the CpG distribution within the 1 Kb sequence window.
GroupScan Analysis in the Simmonic software package was used to plot the recombinant constitution of W29 along with other five related sequences (window = 200, step = 50).
We calculated analogous p-values when comparing the overlap of common word signals in a WPH set with the predicted TFBSs across the seed sequence window.
During the training process, each sequence window was considered as an individual training example and given a score, i.e. the ANN or SVM output.
The ratio of the number of uniquely aligned reads in paired tumor and normal samples for any given genomic sequence window is an estimate of the copy number change in the window.
The matrix-specific SS value of each DNA sequence window was calculated by adding the PWM-determined scores corresponding to each of the respective bases within the window as described previously [31].
A total of 38 smoothed features by a sequence window.
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