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"It was a code I myself had invented!" he wrote in an unpublished manuscript, quoted in a 1986 Discover profile.
Novel TFBS motifs were identified by Discover profile tool of RegPredict using sets of potentially co-regulated genes.
We used the "Discover profile" tool of the RegPredict web-server [ 43] for reconstruction of EBP binding motifs.
For regulons with originally unknown TFBS motifs, we collected a set of upstream regions of known TF-regulated genes and their orthologs and used this set for TFBS identification by the Discover Profile tool in the RegPredict.
Then, for each set of upstream DNA sequences, we used the expectation maximization algorithm implemented in the Discover Profile tool of the RegPredict server [ 64] to identify a common palindromic motif with the highest information content and construct a PWM.
Briefly, EBP binding motifs identified in this work were used for a whole-genome search in upstream regions of coding genes (from −650 to +50 with respect to the translation start) with a threshold equal to a minimal score among all sites reported by the "Discover profile" tool for the motif.
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The most widely used algorithms for finding motifs obtain a generative probabilistic representation of these over-represented signals and try to discover profiles that maximize the information content score.
Note that, without this time discretization and adopting a finer granularity (e.g. a time slot every hour) the discovered profiles would not be sufficiently easy to read, this because we might have duplication of profiles for customers shopping in the same time slots.
They search the neighborhood regions of the initial alignments to obtain locally optimal solutions, which improve the information content of the discovered profiles.
Next-generation high-throughput RNA sequencing technology (RNA-Seq) is a recently-developed method for discovering, profiling, and quantifying RNA transcripts with several advantages over other expression profiling technologies including higher sensitivity and the ability to detect splicing isoforms and somatic mutations [ 16].
Since almost 50% of the loci were unchanged in the present population, it was of interest for us to compare the discovered profiles with those of other ethnic groups, as a test for the robustness of the DMET platform as a potential global clinical tool.
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