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Five cDNA-AFLP protocols were compared for each cDNA sequence collection: classical protocols with one and two enzyme pairs (coverage was calculated using a merge of both fragment sets in the latter case); sequential digestion protocol with two and three releasing enzymes; and a "flip-flop" strategy, in which marking and releasing enzymes swap their roles.
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We performed steps 1 5 of the popLowess stratification procedure on each case using a merge cluster criterion of M = 0.3.
Xenopus, human, and mouse annotations for both coding- and non-coding gene sets were retrieved from Ensembl which uses GENCODE, a merge of the automatic annotation from Ensembl and the manually curated annotation from Havana.
Genome Segmentation : based on genome-segmentation states using a consensus merge of segmentations produced by the ChromHMM and Segway software.
Differential interference contrast (DIC) and fluorescent images were captured and processed using deconvolution microscopy and a merge of the captured images is presented on the far right pane (merge).
In fact, COG [ 7] uses a hierarchical merging of clusters and a manual validation to prevent chaining of multi-domain families.
A merging of time series data using principles of Dynamic Time warping (DTW) has been described in [151] where the time series pair participating in the merge have been optimally aligned using principles of Dynamic Programming if the lengths of the time series pair have not been observed as same.
To remedy over-splitting, the expanded clusters were merged using a modification of the procedure described previously [ 48].
Moreover, we have extended some methods (e.g., using merging of segmentation results in both the wavelet-based smoothing and CGHseg) to accommodate the latest recommendations [12] and needs in the field (e.g., mapping to gain/loss/no-change to allow interpretation based on type of alteration).
Data will be checked and cleaned again using Stata following merging of files.
Post-processing included read trimming with Trim Galore, alignment using Bismark, and merging of informative reads from both strands for CpGs.
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