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The discrepancy may most probably be due to the similarity cutoffs used to determine duplicates, which are reflections on the age of duplications.
So the data are raw — and that leaves investigators with the arduous task of combing through it, figuring out which names are duplicates, which are misspelled or mistakenly listed.
CD-HIT-454 takes raw 454 reads and identifies the artificial duplicates, which are commonly present in 454 pyrosequencing reads.
Integration of these datasets allowed us to systematically study the fates of all gene duplicates which are involved in protein complexes.
The teleost and amphibian NCX2 gene duplicates, which are not much smaller than the mammalian homolog, average 22 kb close to the NCX4a gene and NCX4b at 30 kb.
To better understand buffering by duplicates, we compared the properties of a subset of duplicates which are likely to buffer for each other's function to those which do not buffer for each other.
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Then, α WGD duplicates were updated according to another study [ 44], to exclude tandemly-duplicated WGD duplicates which were shown to have very similar evolutionary patterns with tandem duplicates [ 45].
PCR duplicates, which were produced during library preparations, were removed using MarkDuplicates from Picard program (https://broadinstitute.github.io/picard/) as well as PickingBases, newly developed by one of us (KK) (see Supplementary Perl Scripts S1).
The components of this matrix M × 1 as shown in Fig. 3 present the number of machine duplicates which is removed from cells and moved to machine depot.
The components of this matrix M × 1 as shown in Fig. 2 present the number of machine duplicates which is returned from machine depot to cells.
These were then screened for duplicates, which were subsequently discarded.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com