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We identified a set of DE transcripts among root samples using high throughput replicated sequence data.
Accordingly, the structure of the fluorescent signal of each identified region was noted: either singlet (S), denoting a non-replicated sequence, or doublet (D), disclosing a replicated sequence.
The structure of each signal, either singlet (S), representing a non-replicated sequence, or doublet (D), disclosing a replicated sequence, was noted.
Hence, in most cases where mutations occur, the replicated sequence is hit by a single mutation (P(1) = 0.047).
Accordingly, following hybridization, the fluorescence signals are divided into two categories, a single dot-like signal (designated: "singlet" or "S"), representing a yet non-replicated DNA sequence and a duplicated bipartite signal (designated: "doublet" or "D"), indicating a replicated sequence.
Replicated sequence differences observed in the mature sequence of both miR172 and miR-390 suggest the existence of multiple miR172 and miR-390 family members in cotton, and potentially, there are different miR172 and miR-390 members functioning at different DPA periods.
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The artificially replicated sequences that were an artifact of the 454-based pyrosequencing technique were identified and eliminated using the Replicates software (Gomes-Alvarez et al. 2009).
Replicates [ 79] software was used to identify and eliminate the artificially replicated sequences produced during the 454-based pyrosequencing.
Plotting transcript fold changes levels shows a high correlation among the biologically replicated sequencing runs as indicated by Euclidean distances.
The replicated sequences matched those obtained in the Florence laboratory (see Table S2, see Additional file 2).
We conducted the unsupervised hierarchical clustering analysis using R programming language (version 2.15.1) to evaluate batch effects among 92 replicated sequencing experiments.
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