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The "neofunctionalization" class, containing nine (0.10%) homoeologues was identified with by the existence of both expression evidence and K a /K s > 1.
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Protein-coding genes on novel sequences were predicted using MAKER65, a gene prediction tool combining ab initio predictions, expression evidence and protein homologies.
The sheet "incomplete expression evidence" contains a subset of the data for the 223 loci that include the following: all splicing variants for four loci that lack FL-cDNA or EST expression evidence and at least one splicing variant for 219 loci that lack expression evidence.
All the selected genes had EST expression evidence and covered six phylogenetic groups.
Literature-based causality query, co-expression evidence and alternation of binding free energy also proved that our method is plausible.
In addition, due to mutation of the catalytic triad and no expression evidence, Bmae6 and Bmae28 may be pseudogenes.
It is important to note the difference between non-expressed reactions (expression evidence strongly suggest the absence of such reactions) and non-gene associated reactions (expression evidence not applicable).
There is also expression evidence for MND1 and HOP2 from EST and/or tiling arrays (Additional File 2).
We tested whether there was any correlation between the transcript expression evidence we obtained and the presence of the critical residues described above (Tables 1, 2 and 3).
Jones, T. I. et al. Facioscapulohumeral muscular dystrophy family studies of DUX4 expression: evidence for disease modifiers and a quantitative model of pathogenesis.
BayMiR makes this prediction by integrating sequence and expression evidence.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com