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For all the images of a cycle, silhouettes are segmented based on a depth map.
This requires a linear algorithm based on a depth first search.
We predicted CNVs based on a depth of coverage approach (Yoon et al. 2009) by mapping the reads from the sequenced strains onto the reference.
The overall score for each protein is based on a depth for which the negative log10 of the score is maximized, corresponding to an optimum for the working size of a candidate protein family.
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Also, for small problem instances, an exact algorithm based on a depth-first search to enumerate schedules/placements and find the best one, may be feasible.
The method is based on a depth-first technique with bounding criteria.
LUCY then identifies the vector spliced or ligated to the input sequence based on a depth-first search algorithm, which gives a stringency of 95% minimal sequence similarity.
CNVs were called based on a read depth or depth-of-coverage algorithm provided by Complete Genomics.
The background model is based on a multidimensional (depth and RGB colors) histogram approximating a mixture of Gaussians, while foreground extraction is performed via background comparison in depth and normalized color.
To exclude the contigs derived from contaminating organisms we performed a two-step selection based on a read depth and similarity to known flowering-plant sequences.
Custom written script was used for additional sorting and filtering of the pileup output based on a nucleotide depth cutoff of 10 for each SNP.
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