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Ultimately, to maximize sequence coverage and successfully locate the putative apratoxin A biosynthetic gene cluster, it was necessary for us to use both MDA-generated genomic information and traditional library screening methods.
To maximize sequence coverage, three equivalently loaded and excised gel bands of 0N3R tau were separately digested with trypsin, chymotrypsin or GluC.
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A subset of 472 SNPs was chosen for further analysis by maximizing sequence coverage of 1 SNP per contig.
These data demonstrate that the inclusion of guanidine and acetonitrile in addition to surfactants maximizes overall digestion specificity, total number of peptides, average sequence coverage among all proteins, and the sequence coverage of the TM domain.
To maximize assembly efficiency, a minimum of 25x and maximum 400x sequence coverage at RAD SE reads were imposed.
To maximize the accuracy and prevent false-positive SNP detection, sufficient sequence coverage is necessary and stringent criteria have to be applied to the pipeline.
Inclusion of cultivar-specific gamma gliadin sequences in databases maximizes the number and quality of peptide identifications and increases sequence coverage of these gamma gliadins by MS/MS.
To maximize efficient assembly of sequences we imposed a minimum of 50x and maximum 750x sequence coverage at any RAD sequence cluster.
A possible application would be the combination of data from multiple affected individuals within a single pedigree in order to maximize the probability of sampling a risk-associated allele in the context of low overall sequence coverage.
The sequence coverage depth of 23 was empirically selected to enhance gene coverage and thereby maximize the number of gene with corrected deviation.
Together these results indicate that an optimum amount of sequence coverage can't be inferred from these results, and that the optimum coverage in terms of maximizing numbers of peaks and MACS1.4 score lies outside the upper range of sequencing coverage examined in these experiments.
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