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We calculated three delta indices, PΔ1039, PΔ4069, and PΔ7099, for time periods 2010 2039, 2040 2069, and 2070 2099, restricting the ranges of climate values for future projections to those of the training models to avoid spurious prediction.
These observations implicate that spurious prediction of extra exons in the annotated genes is the major cause of inconsistencies.
Another possible source of error is the spurious prediction of CDSs in long, non-coding RNAs, which has been previously shown to occur [ 44, 45].
For example EC 3.2.1.21 represents a non-specific enzyme class for beta-D-glucosides, allowing for spurious prediction of specific carbohydrate degradation pathways.
To avoid spurious prediction, four widely used software platforms, PicTar [ 33], miRBase Targets version 5 [ 34], TargetScan [ 35] and microRNA[ 36], were used to perform the target prediction.
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As expected, since short ORFs contain more spurious predictions, we observed that as the length increases more ORFs fall in predicted protein clusters.
Thus, it is unlikely that our analysis is biased due to spurious predictions of multiple and/or short coding fRNAs within conserved genes.
Nup37 is found in metazoa and some ascomycetes, suggesting either that we have failed to find all orthologs, or that this Nup has been subject to a series of losses in the Opisthokonts — the recent identification of a Nup37 homolog in Aspergillus nidulans [40] confirms these ascomycete candidates are not spurious predictions.
Such spurious predictions could arise from unrecognized repetitive elements and/or splitting of genes between scaffolds.
For these reasons we rather believe that these sequences correspond to spurious predictions.
Because this ambiguity cannot be resolved in principle, the commonly used best-hit assignment easily results in many spurious predictions.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com