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The identification of repetitive elements is powerful, capable of resolving bacteria at intraspecies levels.
The early identification of repetitive genomic loci in Haloferax species was instrumental in igniting interest in CRISPR Cas systems.
The identification of repetitive elements has traditionally relied on in-depth, manual curation and computational determination of close relatives based on DNA identity.
The identification of repetitive turn structures is therefore a valuable approach to predict polypharmacology or identify backbone conformations that could easily be replaced by mimetic building blocks [4].
The procedure was two-step, including identification of repetitive elements and identification of gene structure.
Furthermore, the most common results of "de-DUFing" included identification of repetitive domains such as ARM, TPR, beta-propellers etc.
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For identification of DNA repetitive elements, we screened the Triticeae Repetitive Elements Database at GrainGenes (TREP) [ 32], Rice Genome Annotation Project Database [ 40], NCBI non-redundant nucleotide databases [ 62] using the BLASTN algorithm [ 33] with a cutoff value of 1e-5, and RepBase [ 34] using CENSOR program [ 35].
A rapid procedure to identify repetitive DNA is based on c0 t DNA isolation [ 8], which is an efficient method for the detection of major repetitive DNA fractions as well as for the identification of novel repetitive sequences in genomes [ 9].
During the first half of the 20th century the identification of the repetitive sequence was largely a matter of subjective judgment.
The identification of novel repetitive sequences was an aim of the c0 t-1 analysis.
Several additional methods were included to complete the identification of putative repetitive elements in the BAC assemblies.
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