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We compared these results to masking based on the curated MIPS REcat repeat library.
Additionally, the intraspecific dot plot of the giant panda yielded some small homologous plots (Figure 3B), which were probably giant panda- or MHC-region-specific repeats because repeat masking based on Carnivora common repetitive elements failed to reveal them before dot plotting.
Converted into an index of mathematically defined repeats (MDR) the low-pass genomic shotgun sequence dataset proved to be as efficient as traditional repeat masking based on BLAST searches.
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The output map was masked based on the actual forest distribution as defined by the CORINE Land Cover database.
Alignments were constructed using Muscle v3.6b [ 109], and masked based on the Muscle alignment scoring function.
Repeat and coding regions of each block were masked based on the annotations of Ensembl database.
The corresponding dodeca image was then masked based on the identified 359 signals, and the remaining dodeca FISH signals were identified based on size and intensity.
A consensus sequence of the aligned contigs is produced, which can be masked based on base call proportion and coverage depth; single nucleotide polymorphisms (SNPs) can be masked similarly using separate user specifications.
Next, the corresponding 359 or dodeca FISH image was masked based on the identified nuclei, and FISH signal intensity was enhanced to increase the contrast between staining and background.
To eliminate artifacts introduced by regions of low ChIP signals caused by poor mappability, regions of no RNAPII sequence coverage were masked based on their mappability scores from the ENCODE Duke Uniqueness 35 bp track.
These topological architectures can be interconnected to constitute many complex optical cryptography networks, and the plaintext can be fully encrypted into phase-only masks based on any one optical encryption strategy selected from the cryptography network.
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