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The gene ranking for WAD was also the most consistent when subsets of top-ranked genes produced from three different preprocessed data (MAS, RMA, and DFW) were compared.
These data suggest that the two genes produced from the duplication of the original PDCD4 gene during early higher plant evolution might have been the progenitor genes for MAT8 and the MAT5/6/7 subgroups and the latter subgroup underwent expansion in some species.
The phylogenetic trees for these two genes, produced from the bayesian analysis, and on which the various models of the PAML software were evaluated for their goodness of fit, are presented in figures 1 and 2. In the NOS tree only An. merus, An. melas and An.
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These results are derived from a 513 188 amino acid concatenated, gap-free, multiple sequence alignment (~250 aligned amino acid positions per gene) produced from the 2 135 triplets possessing at least a 50 amino acid aligned block.
Surprisingly, 1063 genes produced more RNA from 0.5 to 96 hours after death.
The CEP63 and DEUP1 genes were produced from a single gene locus by gene duplication leading to proteins with related but specialised functions.
A UniGene set of 2800 genes was produced from a cold induced oat cDNA library.
Together, these results suggest that at least part of the siRNAs that matched to genes are produced from dsRNA formed by overlapping sense and antisense transcripts in M. oryzae.
A tentative canonical list of 17,260 nonoverlapping human nuclear genes was produced from the UCSC Genome Browser and used to locate human microsatellites conserved in coding exons, 3′-untranslated regions (UTRs), 5′-UTRs, introns, or intergenic regions (IGRs).
Strict consensus trees were built for each gene using the 100 gene trees produced from bootstrap replicates.
The 3′ end piRNA profile associated with AGAP003387 might be similar to the profile of genes producing piRNAs from their 3′ UTR in D. melanogaster [ 36, 45, 46].
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