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The resulting reads were clustered using CD-HIT-454 [ 102] setting an identity threshold of 0.98 and the accurate mode option g1.
Each dataset was processed separately using the accurate mode (option '-g 1') of the software.
We applied the "accurate" mode (with 'job' arguments: 'de novo, est, accurate') to limit the assembly of paralogous genes.
Assembled transcripts from individual samples were merged and duplicates were then removed using CD-hit-est [ 21] (v4.5.4) using the accurate mode (−g 1) with other parameters left as default to yield the final assembly (Contigs-clustered Assembly).
Multiple sequence alignments were generated with T-Coffee (Notredame et al. 2000) using the "accurate" mode, which combines alignment using structural information with alignment using homology extension (Di Tommaso et al. 2011).
Assemblies of individual samples were merged with both strands information using the accurate mode of cd-hit-est version 4.5.4 with the sequence identity threshold at 100% and a word size of 8 [ 15].
Similar(53)
For the physically accurate mode, it is shown analytically that the numerical dispersion relation is accurate to order 2p+2, where p is the highest order of the basis polynomials.
Clustering was performed in the most accurate mode where each sequence is added to the cluster to which it is the most similar rather than to the first cluster for which the sequence identity threshold is met.
Cells were sorted at the most accurate mode (single cell, one drop) with a sorting speed of 4,000 s−1 and a sample chamber cooled to 4°C.
We used the most accurate mode that uses both sequence and evolutionary profiles.
A mode matching method based on the characteristics of accurate mode shape estimates is proposed to ensure the correctness of the estimates.
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