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For all the sequences we calculated the number of people in the whole frame.
When two slow slip events occurred at a short interval in some sequences, we calculated seismic moments for velocities larger than 10−3 or 10−4 m/s, and we selected the event with the larger seismic moment as a forecast data point.
Then for groups of 200 sequences, we calculated running averages of the fraction of mRNAs with 7mer seed matches in their 3'-UTRs.
For each 500 bp window (shifted by 100 bp) spanning these sequences, we calculated the significance of overlap between its corresponding WPH set and the NRSF-bound sequences.
Based on 514 independent Nef HIV-1 subtype B sequences, we calculated the population frequency of each unique peptide derived from this dataset, i.e., the percentage of sequences with the specific 10-mer.
To detect selection on protein coding sequences, we calculated the ratio of the number of nonsynonymous substitutions per nonsynonymous site (Kn) to the number of synonymous substitutions per synonymous site (Ks) [58].
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To this end, for each of the aforementioned groups of GC-sorted sequences, we calculate an average pressure towards the GC content(s) of interest.
For each of these sequences we calculate the Keq (equilibrium constant) values for the forward and reverse target sequences aligned to every position of the probe.
Then, based on the selected testing sequences, we calculate the precision and recall of EFICAz for each of those enzyme types.
By comparing the sequencing depth of TE sequences to sequencing depth of unique genomic sequences, we calculate a metric enabling us to estimate the entire TE content of a library, both ancient TEs and relatively more recent, undiverged TEs.
Once we have the appropriately trimmed target and germline sequences, we calculate the log of the total probability of a proposed rearrangement using the forward and backward algorithms (Durbin et al., 1998; Majoras, 2007).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com