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Having outlined our approach for structured pattern search, here we tackle the problem of structured profile search.
For structured profile search, only Anrep [ 3, 4] provides the capability to model structured profiles, with its general network expressions.
Moreover, its implementation doesn't support structured profile search.
To our knowledge, SMOTIF is the only implemented method that can handle structured profile search.
Another potential direction is to directly extract structured profile (or position weight matrix) patterns.
For structured profile search problem, we first search each simple motif by aligning its profile with the sequences, and then search structured motifs with positional joins.
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The final integrated dataset consisted of the Entrez Gene Identifier, Gene Symbol, the SNP Identifier, the Amino Acid Substitution, the SVM score computed for the sequence and structure profile models and the structural consequence of the SNP.
Given a reference sequence (structure) profile y, we compared two structural (sequence) profiles x1 and x2 using their Pearson or Spearman correlation coefficients ρ y, x1) and ρ y, x2).
We used previously published datasets of genome-wide RNA secondary structure obtained by PARS (Parallel Analysis of RNA structure)26 to analyze the RNA structure profile in the 5ʹUTRs, CDSs and 3ʹUTRs.
The crystalline structure profile of the compound layer obtained by pulsed plasma nitriding in steel gears is reported.
The paper presents a design exercise of upgrading a typical rock armoured revetment by modifying the structure profile and adding structure elements.
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