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A small number of functional protein sequences selected from binary-patterned libraries suffice as input for the consensus design of active enzymes that are easier to produce and substantially more stable than individual members of the starting data set.
In total, our starting data set comprised 967 putative GH1 encoding genes.
We argue that common presence of such identity elements in the starting data set favours interspecies compatibility.
In our starting data set 333 regulatory interactions formed 111 FF motifs and 28 AL motifs wtih TFs regulating transcription of their own genes.
All further analysis was therefore done using the selection of exon array probe sets based on variance as starting data set.
The starting data set [ 2] comprised sequences from Saccharomyces cerevisiae (Ascomycota, Fungi), plants (Arabidopsis thaliana and Oryza sativa), Dictyostelium discoideum (Ameobozoa), Amphimedon queenslandica (Demospongiae, Porifera), Nematostella vectensis (Anthozoa, Cnidaria), Drosophila melanogaster (Hexapoda, Arthropoda) and Homo sapiens.
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Again, we could not find any obvious correlation between the methods and the size of the starting data sets, neither in terms of target genes nor in terms of binding sites per TF.
Both consensus and supertree methods were used to derive phylogenomic supertrees representing the relationships among the species in our seven starting data sets.
For the remainder of the main text, we first describe in the materials section the starting data sets used, and we then describe the construction of the compound spectra needed for our study.
We produced starting data sets, in which sequences grouped for the 20 identity from bacteria were filtered for the presence of major coli identity elements while eukaryotic sequences for the presence of yeast identity elements.
Before starting data collection, a protocol was set up and discussed with participating midwives to ensure that a uniform protocol was followed by all midwifery practices.
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