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A list of H. influenzae Rd genes whose products regulate competence, contribute to DNA uptake machinery, or interact with incoming DNA has been previously compiled for the 13 strains with sequences available (Table 2; [40]).
A comprehensive list of 149 a priori candidate genes associated with FT was previously compiled for comparison to homologous sequences in maize (Chen et al. 2012).
As calibrations, we used multiple mammalian fossil constraints previously compiled for key nodes [ 48], which include "hard" minimum and "soft" maximum constraints, thus making time estimations less sensitive to the parameters of the prior distributions [ 49].
Therefore, retention factor values previously compiled for other nutrients were always <1 (in the USDA database for example, 100% retention or a value of 1 was assumed to be a maximum and any values in excess of this were rounded down to this figure).
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In addition, a previously compiled bad list for organic compounds in aqueous solution (Meringer et al., 2013) and a preloaded bad list that excludes highly strained ring systems are used, rings of size 3 and 4 are forbidden, and Cl being connected to a carbon atom is prescribed.
We also examined references listed in review articles and previously compiled bibliographies to look for eligible studies.
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We estimated positions of transcriptional start sites using sequences of more than 10 000 independent full-length cDNA clones for each species, which were previously compiled into databases.
The lists of known tissue-specific genes for different tissues were collected from UniProt database, and the expression data retrieved from the previously compiled dataset according to the lists were used for input vector encoding.
They demonstrated a statistical association between SSRs and previously compiled datasets of repeated DNA sequences in six Drosophila species and Anopheles gambiae (a similar compilation for B. mori was not provided).
For HB3 and DD2 lab strains, where we used a previously compiled list of CGH hits [ 19], the FREEC software led to the highest concordance (92.9%) between coverage- and CGH-based hits.
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CEO of Professional Science Editing for Scientists @ prosciediting.com