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Based in the sequence similarity of the sugarcane AGO genes to those of other plant species (data not shown), it is possible that a similar nucleotide preference may exist on sugarcane, and the results in Figure 3 may indicate that the majority of the new 21 nt microRNA candidates identified in this work are canonical miRNA.
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In contrast, our model is based in the sequences of almost all the known proteins displaying prion-like behavior and we have demonstrated that our method can perform as well as PAPA for differentiating real and false prions.
Phylogenetic trees based in rpoD sequences were constructed using the method of Maximum Likelihood.
In conventional Sanger sequencing, the accuracy of the call of each base in the sequence can be assessed using Phred scores, which are probability-based confidence scores (Ewing et al, 1998a; Ewing and Green, 1998b).
This method assigns a probability distribution over labels to each base in the sequence considering ChIP-chip ratio and sequence information.
Dam is a member of this family that selectively modifies the adenine base in the sequence GATC and is responsible for most of the DNA methylation in Escherichia coli [3].
This result is also robust to the underlying sampling variance of the diversity estimates, because bootstrap resampling of the individual bases in the sequence data also demonstrates a significant correlation (median rs = −0.61; 95% CI: −0.87, −0.17).
As each 5 base sequence was encountered, the next two bases in the sequence were added.
The quality of each base in the sequence was assessed with the program Phred [ 54, 55].
All sequencing platform vendors provide quality scores for individual bases in the sequence reads.
CAP3 may yield conflicting bases in the sequence generated for the contig.
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