Sentence examples for true duplication from inspiring English sources
In this hypothetical example, only four gene duplicate pairs representing the true duplication events were retained, while removing the six additional duplicate pairs displaying sequence similarity.
Filamin C (FLNC) appears to be a true duplication, with transcripts divergent at the nucleotide and protein levels.
All trees with four taxa are true duplication trees, thus evaluation of the A domains with the PDH algorithm is trivial.
We also removed shadow pairs within multiple-member gene families, which were representative of sequence similarity rather than true duplication events.
Evidence for the true duplication of 13 immune-related genes: ATF4, CD36, CD68, CD163, CRP, DDX3X, GSTP1, GZMA, IFIT1, IL1B, IRGC, ITLN2, and OAS1, and 5 non-immune genes, appears unequivocal (Additional file 3: Table S3).
One gene, TNFRSF10A, which is listed provisionally here as artifactually duplicated, proved especially problematic since there is equal evidence for both artifactual and true duplication; directed studies will be necessary to determine the nature of this duplication.
However, not all duplicated genes seem to have arisen from true duplications, but some may have been transferred horizontally, like some PTS system genes that are L. monocytogenes EGD-e strain-specific genes.
The reviewers raise the concern that small-scale duplications (either true duplications or due to mis-assemblies) could generate false positives.
It should be emphasized that not all true duplications could be detected by qRT-PCR, especially low-copy duplications with divergent reads ratio > 0.8 are difficult to be detected.
This was taken to reflect annotation errors rather than true gene duplication events.
Besides, since simulation experiments allow us to record the true gene duplication and loss history during data generation, we can also test the accuracy of the refinement algorithms with the true history, without mixing their performance with that of gene tree reconstruction or reconciliation.
