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As most validated MRESSs are located in the 3′UTR of mature mRNAs, we only predicted MRESSs for the 29,962 3′UTR sequences.
We only predicted bivalent promoters for intergenic miRNAs since it was impossible to distinguish whether the features were associated with the ST miRNA or the host gene.
Hence, we only predicted and analyzed the tertiary structure of globin domains from the selected rhizobial GCSs. Figure 5 shows that the predicted rhizobial GCSs globin domain exhibits a 1.5- to 3-turn pre-helix A, that (with the exception of SinfreGR64GCS) no loop exists between helices A and B, and that helix H is unusually long in Rhietl8C3GCS, RhietlCIAT652GCS2 and RhilegGB30GCS2.
Due to the low likelihood of such an event (or series of events), we only predicted a translocation polymorphism when: 1) there was at least one matepair for which the translocation mapping was unique, and 2) for all of the other matepairs, there were no mapped locations that had both ends of the clone on the same chromosome.
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There are two main reasons for the discrepancies with our predicted number of active enhancers: the resolution of the genome segmentation is very different and we only predict enhancers that are active in one condition but not in the other.
Note, however, that we only predict the occurrence of systematic N400 and LPC effects related to decade-consistency (if this effect originates at a lexico-semantic stage of processing), but not their specific direction.
We keep only predicted complexes that are novel, unique, and high-confidence.
The second feature is that we not only predicted YY1-binding motifs from the binding loci but also identified many cofactors that could function together with YY1.
We considered only predicted targets having a miRmap score above 90 and retained, at most, the first 500 with the best score.
We considered only predicted octamers to obtain the PU values on the same scale which would be problematic for elements of different sizes.
We not only predicted 60 Alu-related miRNAs that might be transcribed through Alu, including the previously reported miR-517a, but also identified 23 of them by Solexa sequencing.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com