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The SEAL application was run on all the DS datasets in both alignment-only and alignment plus remove duplicate modes.
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Similarly, in a study of six varying duplication modes by Wang et al. (2011), it was observed that genes duplicated by whole genome multiplication and tandem duplication exhibited more conserved expression when compared with all other modes of duplication.
By looking at the location of duplicated genes in the genome the duplication mode can be assessed.
Among recent duplicates of different modes, transposed duplicates diverge most dramatically in gene structure.
We found that transposed duplicates diverge more dramatically in gene structure than genes duplicated by other modes, and that the structural changes in transposed duplications are biased toward shorter length and lower complexity.
We compared the answers of the duplicate seasons together (mode, median, range, IQR).
Apparently, there are two modes for each duplicate pair: duplicated after the mouse-zebrafish split) or before mouse-zebrafish split).
Two common modes of duplicate gene loss include nonfunctionalization and loss due to population dynamics (failed fixation).
We attempted to separate the effects of different modes of duplicate retention by categorizing the expression profile into four types (see methods) for the seven sets of gene duplicates and inferring their ancestral expression states for a comparison.
Even if a model is identified that can represent well the response of the structure, this model is often a non-minimal realization (i.e., the dynamics of various modes are duplicated in the model); these extra dynamics can degrade the performance of the resulting controller.
All separations were performed in duplicate in full-scan mode for peak capacity determination and a third time in MS fragmentation mode for protein identification.
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