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For each trimming method and each of the three levels of divergence (i.e. ×1, ×2, ×3), a ROC graph (e.g. [ 51- 54]) depicting the plot of the true (y-axis) and false (x-axis) positive rates for each of the 200 datasets is represented in Figure 1.
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As an alternative to the analyses described above, blastx searches for each trimmed EST sequence, without prior contig assembly, were also performed against all Arabidopsis proteins, which generated similar EST hit ratios for the same genes as the analyses above.
Neighbor-joining trees were constructed for each trimmed alignment as implemented in BioNJ [ 36], and T. brucei protein sequences were used as the out-group.
For each character trimming method and each level of divergence, we computed the distribution of the so-obtained bootstrap-based confidence values, as well as its average value.
The Maximum Information algorithm determines the combined score of the three factors for each possible trimming position, and the best combined score determines how much of the read to trim.
The reads produced by the 454 Titanium sequencing were each trimmed for poly-A/T tails and 454 and SMARTer adapter sequences (in-house tool, based on a multi-pass Blast and heuristics), with reads trimmed to less than 50 bp removed.
The 16 configurations were modelled with two different approaches: generating a new mesh for each trim condition (standard method) and using a morphed version of the baseline condition.
One directional trim cut can be written as a main program which calls a separate sub-program NC file for each trim cut to reduce the NC program size.
Briefly, 1 kb of DNA upstream of the predicted transcription start site for each TRIM protein along with 100 bp reading into the mRNA (−1000 bp to +100 bp) was selected from the human genome for analysis.
Studies to identify substrates for each TRIM protein.
Thirteen professional claw trimmers were specifically trained by the authors in a course immediately before the claw trimming visits, as well as by individual training for each trimmer in one or two herds at the start of the project.
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