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From these results, we can estimate the number of putative false positives and false negatives that might have been caused by sequence variation.
Given that most of the probes showed a higher copy number in the BLG2 and MSM strains than in B6, the strain that was the source of the sequence information, the difference of the CNV values was unlikely to have been caused by sequence polymorphisms.
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The 2-fold lower frequency of R3a relative to R3b is unlikely to have been caused by sequencing bias and instead probably reflects real in vivo stoichiometric differences.
Moreover, because many of these mismatches could have been caused by sequencing errors and false mapping of scnRNAs that were produced from loci outside of the LMR locus, the frequency of base replacements was likely overestimated.
However, as the quality scores were not available for all ESTs used in the analysis, the putative SNPs could have been caused by sequencing errors as well as the true SNPs.
To reduce false negatives that can be caused by sequence variability, a new universal primer pair was designed against a divergent sequence data set, targeting the open reading frame 4 (heat shock protein 70 homologue gene), and optimised for conventional one-step RT-PCR and one-step SYBR Green real-time RT-PCR assays.
Collectively, these diverse mapping data sets demonstrate that expression of Comt is strongly cis-regulated and is caused by sequence variation in or around Comt itself.
The identified SNPs in positions of downregulated probes suggested that the observed downregulation of Spr mitochondrial genome is caused by sequence divergence.
To suggestively analyse whether differential methylation of specific loci are caused by sequence differences we decided to study its genetic stability and segregation over several generations.
Thus, artifactual "under-representation" of these regions would be caused by sequence divergence in the UTRs beyond the point of blast-detectable similarity and not by the actual bias against UTRs in our sequences.
Alignments of the deduced amino acid sequences of these Floydiella genes with their homologs in the Chlorophyta and the Streptophyta revealed that their expansion is caused by sequence insertions at one or more sites within internal regions.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com