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To be conservative, we removed predictions for which the shuffled alignments were also classified as structured RNAs with an above-cutoff classification confidence.
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To incorporate chromatin modification signatures as additive information, an additional filter is applied to remove predictions that are not supported by the histone evidence.
However, in our experience, removing predictions that involve multi-mapping contigs is useful in reducing false positives in real data.
A minimal agreement of MDBs and a minimal coverage were adopted to remove predictions that are based on insufficient support.
We suggest that users have Barnacle remove predictions involving multi-mapping contigs, unless specifically looking for events involving genes within known segmental duplications.
With the predictions, we used this probabilistic measure to remove predictions with an associated ambiguity for the class assignment (the probability of membership of the given class was <0.95).
Row 1 in this table contains values with a configuration that uses BLAT for contig-to-genome alignments and BWA for read-to-contig alignments, and has Barnacle remove predictions involving multi-mapping contigs (see Stage 3, filter 2).
Furthermore, we removed EvoFold predictions that were shorter than 10 nucleotides because the vast majority of predictions that were less than 10 nucleotides were not likely to form a stable RNA secondary structure.
These were removed from predictions using the Tables function of the UCSC genome browser (http://genome.ucsc.edu).ucsc.edu
Signal peptide sequences were removed following predictions of cleavage site location made by SignalP 3.0.
The experimental validation of SHEAR's reported SV breakpoints confirms that the removed CREST predictions were indeed false positives.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com