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In 81% of simulated coordinated coding datasets, shuffling significantly changed the distribution of sequence correlations.
(E ) Results of a corrected shuffling procedure applied to simulated independent coding datasets and an experimental dataset (height magnified for comparison).
The syntenic anchor dataset was built by combining the miRNA and protein coding datasets, where each anchor is identified by its family name.
When applied to experimental data from CA1, the shuffling test failed to detect any significant effect of shuffling (t-test, p = 0.28, 2436 events), as in most (74%) of the simulated independent coding datasets.
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We annotated our assembled pool of R. pomonella sequences (contigs and singletons = 100) to the non-redundant D. melanogaster protein coding dataset.
FM carried out the analysis on coding dataset, participated in the design and coordination of the study and helped to draft the manuscript.
Phylogenetic trees were generated using the neighbour joining algorithm and Kimura's two-parameter distance using nonparametric bootstrapping with 5,000 replicates from the total (noncoding and coding) dataset in the MEGA4 package [ 25].
Compared with non-gap-coded datasets, gap-coded datasets only slightly altered the support values (either increased or decreased) and topologies, regardless of weakly supported or collapsed nodes (results not shown).
Following an accurate benchmark on controlled coding and non-coding datasets, CPS thresholds for coding and non-coding CSTs were evaluated.
As is evident from the open-source codes, datasets analyzed through CrossCheck are never copied or stored, therefore providing complete confidentiality of the users' unpublished data.
To this end, the source code, datasets, and results are freely available at http://tavazoielab.princeton.edu/FIRE-pro.
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