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Furthermore, our data albeit at a much smaller sequencing scale emphasize targeted re-sequencing as an effective approach to perform high-throughput genotyping in tumor samples.
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As a final test, we tested MetaPSICOV on a set of target proteins with much smaller sequence families than the original PSICOV test set (see Supplementary Table S2).
Undersampling methods, in contrast to oversampling methods which replicate the number of sequences, have the advantage of working with a much smaller number of sequences which appreciably reduces computational processing.
For DNA-targets the sequence correction is of much smaller impact because of smaller sequence-induced variability of the raw intensities.
The HGP was visionary, initiated even before the first bacterial genome (much smaller) had been sequenced.
The scaffold sets from SOAPdenovo, MaSuRCA, CABOG and Bambus2 contain much smaller numbers of sequences than their corresponding contig sets.
And the size of 2A peptide coding sequence is much smaller than that of IRES sequence.
Other rheumatic disease studies have conducted much smaller scale whole-genome sequencing in one to five individuals followed by targeted exome or Sanger sequencing of the identified variants in larger samples [ 13].
In accord with the finding in our earlier study of a much smaller set of NifD sequences, the patterns of conserved residues in the twelve-residue sequence that includes Cys-275 or in the nine-residue sequence centered on His-442 allow unambiguous assignment of a NifD sequence to either Group I or Group II (Tables 1 and 2).
However, it is well within the range of other plants whose genomes have recently been sequenced, such as sorghum (∼730 Mbp) or pigeon pea (∼833 Mbp), and indeed much smaller than the now sequenced 2.3 Gbp of the maize genome (Paterson et al. 2009; Schnable et al. 2009; Varshney et al. 2011).
From these graphs, we can see that the new method improves discrimination by assigning much smaller binding probabilities for sequences with no known binding sites (no matter whether AUC or AUC30 is used), which thus results in much smaller false positive rate.
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