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In the Introduction we described three well-studied models have been used to characterize searching behavior (Fig. 1).
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The aerobic gut bacteria of C. pomonella were isolated and characterized searching for bacterial control agents which may be used against it.
Annotation extensions: when the original Pfam v. 21 annotations were used to characterize searches with our hard and sampled queries against the target library, thousands of alignments to very similar UniProt sequences (e.g. E < 10−80, with >95% identity) were annotated as partial homologs or non-homologs.
Moreover, fast, global optimization techniques need to be deployed to provide the best design options, for a given application, within a well-constrained and characterized search space.
To better characterize similarity searching strategies, in particular, PSI-BLAST performance, against comprehensive protein databases, we identified a set of diverse protein domains from Pfam (Finn et al., 2010) v. 21 to use as queries against a set of real proteins containing those domains.
Putative cis-elements on the OsSUT2 promoter sequence were characterized by searching for similar motifs in the Database of Plant Cis-acting Regulatory DNA Elements (PLACE) (Higo et al. 1999).
These properties make εA an excellent substrate for characterizing the searching mechanism of AAG.
Osr22, Osr31 and Osr38 were originally characterized by searching part of the rice genome sequence [ 28].
Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs.
The gene products encoded by the 4,709 ORFs were characterized by searching for sequence similarity with known bacterial proteins contained in various collections.
Developing biomarkers is often characterized as searching for a diagnostic gold standard that can seem appealing in its promise of certainty.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com