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Furthermore, a study of human genes involved in disease found lower non-synonymous substitution rate (KA) in the disease genes compared to generic genes [ 5].
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Gene Ontology (GO) searches were performed with the Generic Gene Ontology Term Finder (http://go.princeton.edu/cgi-bin/GOTermFinder) [47].
In order to characterize the biological design principles governing such switches, we have developed mathematical models of generic gene circuits and analyzed their behavior.
Nonetheless, the official (generic) gene name will be written in all capital letters and the dominant/recessive behavior of particular alleles will be recorded as attributes of the alleles, rather than as part of the gene name in the database.
Minimal editing, such as minor repositioning of nodes and removal of few exceedingly generic gene-sets (e.g. Protein Complex Assembly, Biopolymer Catabolism), was done to optimize the map layout.
GO term enrichment analysis in the investigated genes was carried out using the Generic Gene Ontology (GO) Term Finder online tool available at http://quantbio.princeton.edu/toolsResources.html.html
Significantly shared GO terms among the selected proteins from the Protoarray screen were identified with the Generic Gene Ontology (GO) Term Finder at the Lewis-Sigler Institute at Princeton University (release 27-Jan-2009; http://go.princeton.edu/cgi-bin/GOTermFinder, [50]) based on annotations in the Saccharomyces cerevisiae Genome Database (SGD).
Classification of proteins was made using the software GENERIC GENE ONTOLOGY (GO) TERM MAPPER [ 24].
Considering two generic gene sets X and Y the two measures are defined as follows.
This is particularly important for generic gene names, such as for example kinase.
The Generic gene browser, GBrowse, JMOL for structural visualization and TREEVIEW for phylograms have been integrated for clear perception of retrieved data.
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