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As anticipated with hexamer-primed cDNA synthesis, the distribution of sequence alignments along transcripts appeared random.
So far, computer simulations were required for statistical inferences on the distribution of sequence motifs.
The sequences are loaded, and the distribution of sequence lengths is displayed.
The size distribution of sequence reads peaked at 23 nt (Fig. 1), which was consistent with the ideal size of genuine miRNAs.
Applying weighting to sequence tags depending on local GC percentage eliminated most variations in the distribution of sequence tags across each chromosome.
The weighted number of sequence tag within every 50 kb non-overlapping window was then summed to obtain the distribution of sequence tag density for each chromosome.
Figure 2A shows the distribution of sequence tags across each chromosome before and after correction for GC bias for one of the 19 samples.
Previous comparative sequence analysis revealed an interesting and unusual distribution of sequence variation across the CTV genome [11], [12], [16], [34].
The distribution of sequence length in these two modes reveals that Phyre typically achieves greater sequence coverage for longer protein sequences (Figure 1B).
To test the contribution of DNA uptake bias to the observed distribution of sequence frequencies, I wrote the Perl based program Genome_Dynamics.pl (program available on request).
Simulations of DUES evolution in hypothetical genomes subjected to mutation and uptake bias towards the DUES only fail to reproduce the observed distribution of sequence overrepresentation across mismatch loads, whilst consideration of additional uptake bias towards mismatched sequences did.
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