Exact(1)
To evaluate the classification error associated with UFM, it is necessary to first consider that the error may concern 3 factors the diagnosis of the coding status (coding or not coding), the coding strand, and the coding frame.
Similar(7)
In the particular case of P. falciparum, which exhibits an extremely rich AT content, LORF was even more efficient than UFM; however, it has no discrimination power between coding vs. non-coding DNA.
21 Filtering out these false positives should only be considered on a case-to-case basis because it would affect the universality of UFM seeing as it would affect its applicability to other species without previous knowledge.
The optimal threshold values of CDS/intron classification by CSF (τ CSF) and UFM (τ UFM) were estimated by fixed-point optimization 35 of the harmonic mean of sensitivity and specificity.
This line does not participate in the UFM classification process; it is only used as a guideline to facilitate plot-to-plot comparisons.
Finally, we evaluated the performance of UFM by comparing it to the success rates of the classification of coding sequence, strand, and frame diagnosis of the largest ORF (LORF) of the sequence considered.
Sample UFM mode (S-UFM) was implemented by exciting the ultrasonic vibration at the tip-TiN sample contact using a piezotransducer bonded with polycrystalline salol at the back of the coated stainless steel disc.
By contrast to filter 1 and filter 2, filter 3 cannot be inserted in the UFM algorithm a priori because it is not only true in >94% of frames +1 of complete CDSs (data not shown), but also in ~60% of their frames −1 with the consequence that it would come into conflict with the success rate of coding frame diagnosis (data not shown).
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