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It is widely believed that deep sequencing coverage (multiple independent sequences for the same locus) should make it possible to correct for errors in this context [ 16].
An advantage of the great diversity of elements is that with a single PCR, cloning, and determination of multiple clone sequences one retrieves multiple independent sequences with which to do phylogenetic analysis.
Therefore, we have specifically analyzed the methylation status of multiple independent sequences from the FSHD1-associated D4Z4, which is important because in FSHD1 only the contracted 4q D4Z4 array shows epigenetic changes [ 76].
Additional transposable elements could serve as phylogenetic markers in a manner similar to ERV-L in the present study, while providing multiple independent sequences to test ordinal level phylogenies.
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The performance of multiple independent sequencing reactions on single amplified samples permits the identification of common sequences, providing increased confidence in their authenticity.
To overcome the dataset dependency nature of F-score calculations, we selected sequence features that consistently have the highest F-scores across multiple, independent subsets of sequences.
As an assay, whole genome shotgun sequencing can be simpler than MLST, which requires multiple independent PCR and sequencing reactions to be performed for each sample.
Multiple independent clones were sequenced from each PCR product within each cell line (see Supplementary file 2 for primer sequences), of which six representative clones are displayed.
The predicted deleterious effect of each nsSNP was measured taking into account multiple independent parameters including sequence conservation, effect on structural stability, proximity to phosphorylation sites, glycosylation sites and disulphide bonds (see Supporting Information S1).
For 21 transcription factor genes there was strong evidence for this gene structure being the sole mechanism for generation of alternative transcripts, with multiple independent ESTs (expressed sequence tags) identified for each transcript.
To the best of our knowledge, this is the first study that uses Next Generation Sequencing Technology to sequence multiple independent genetic loci from feces to infer species boundaries in endangered or critically endangered primates.
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