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The pig origin of 115 orthologous miRNA was confirmed by alignment of each specific pre-miRNAs to the pig genome (Table S2).
Novel ASV were identified by alignment of each cloned sequence to its respective genomic sequence in comparison with full-length transcripts.
Thus, mutations were not assigned to individual plaques; rather, all mutations within an individual mouse were identified by alignment of each read against the lacZ gene.
Genome coverage and copy number estimations for each element were calculated by alignment of each repeat to the assembled genomes using RepeatMasker.
For the bioinformatics analyses, computational analysis of alternative splicing was performed by alignment of each cDNA sequence to its respective genomic sequence using SIM4 (software for analysis of splice variants; Pennsylvania State University, Centre County, Pennsylvania, USA).
Novel splice variants were identified by alignment of each cloned sequence to its respective genomic sequence in comparison with full-length transcripts of sequence databases of National Center for Biotechnology Information (NCBI) using the splice variant analysis software SIM4 [ 47].
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Consensus sequences were generated by alignment of all intact copies of each retrotransposon (Additional file 2).
The specific sequences were selected by alignment of all sequences available for each virus from the National Center for Biotechnology Information (NCBI) GenBank Database.
The specificity of each primer set was confirmed by alignment of dissociation curves.
The location of DG markers on each chromosome was determined by alignment of DG sequences with the reference genome.
The consensus sequence for each gene fragment was determined by alignment of the forward and reverse sequences using BioEdit version 7.0.5.3 (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
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by coupling of each
by multiplication of each
by saturation of each
by weight of each
by resolution of each
by summation of each
by homogenization of each
by number of each
by location of each
by way of each
by discussion of each
by default of each
by complement of each
by normalization of each
by sum of each
by detection of each
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