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We identified potential gene conversion events within each subfamily using the methods implemented in the GeneConv program [ 51] which identifies identical fragments shared between pairs of nucleotide sequences.
To do this, Suspenders first identifies identical mappings based on the mapping start position in the reference genome (chromosome and coordinate), its cigar string in the reference genome, its pairing (either paired or unpaired) flag, its fragment end flag (either first or second) and its quality score [e.g. the Bowtie end-to-end score (16)] from the pseudogenome mappings.
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Second, very high cutoff scores (e.g. BLAST scores of 0 plus 100% of identity) will allow for instance to identify identical sequences dispersed over long geographical distances.
Furthermore, investigating the oscillatory behavior of the entropy and complexity time variation, the periodicity of 3.67 years was identified, identical to one of the main periodicities revealed in the Multivariate ENSO Index (MEI).
Overall, the two approaches proved to be highly complementary; both assays identified identical detergents that produced active solubilized CCR5 as well as those detergents that either were ineffective solubilizers or inactivated the receptor.
Students could generally identify identical trees showed the same branching pattern of relationships despite node rotations.
The, conflicting switch for SNPduo++ can also identify identical samples and first degree relationships.
Although the random-ascospore progenies that resulted from the crossing protocol minimized the isolation of twin isolates, the large number of markers identified identical progeny efficiently.
We identified identical matches near the start site in promoters for two genes: one for NvClock (-225 bp) and two for NvCry1a (−526, −526 bp).
To determine whether PCR recombination can give false-positive evidence of intramolecular recombination, we identified identical or near-identical regions shared between the Vigna and Cucurbita (GenBank GQ856148) mitochondrial genomes (Table S2).
As for the viral tags, small RNA sequences expressed by Sus scrofa were first grouped to identify identical reads and to define the counts associated with particular sequence tags.
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