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We could not distinguish a true sequence difference from differences introduced by amplification errors or biases below this threshold.
Now, given the observed count of the alternative allele at that position r i, one can compute the probability of r i being produced by sequencing errors as: Only if P i pois stays below a certain threshold, e.g. Bonferroni corrected threshold of 5%, then the observed count of the alternative allele at position i is due to a true sequence variant.
The second error rate estimate is based on the median (b=3×10−4), and is used together with the allele frequency to be detected f for modeling the fact that some erroneous reads of the major allele can contribute to a true sequence variant.
Hits against a true sequence of a different family are considered to be neither true positives or false positives, because there are known to be evolutionary relationships between at least some of the ncRNA families, but these are not all well characterized.
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In the context of this manuscript, we make the assumption that there is a single "true" sequence of events or organization of matter on the temporal and spatial biological scale (i.e., Life on Earth).
It is unclear which mature sequence is a true miRNA sequence.
These likely represent an underestimation of true sequence diversity of the species because they lack multiple serotypes (e.g. 3a, 3b, 3c, 4e, 7), less stringent similarity cutoffs and a lower number of fully sequenced strains.
Unexpectedly, all evaluated tools failed to identify a large proportion of true sequence variations (false negative SNPs).
We note, however, that there is an issue regarding the true sequence boundaries: while benchmark test for sequence structure alignments are usually given as full-length transcripts, this setting is quite unlikely in practical application scenarios, where one often has either a partial transcript (e.g. from RNA-seq data), or just transcripts with wrong boundaries.
First, there is not one true sequence for a species because of individual genomic variation.
The aim is for the e-graph to contain a path corresponding to the true sequence, ideally terminating close to the end of the desired chromosome, and for this path to be identifiable as the best.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com