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The remaining reads continued in the pipeline to be screened for repetitive elements, using the program RepeatMasker 3.2.9 (http://www.repeatmasker.org) against PlantRepeatsDB [ 32].
We estimated the times of insertion for Gypsy and Copia elements using the method described by SanMiguel et al.25 (Fig. 2e and Supplementary Fig. 20).
The aim of this paper is to present a formalization of the MDE elements using the Theory of Institutions.
The algorithm includes section subdivision into trapezoidal elements using the techniques of polygon clipping algorithm proposed by Weiler Atherton.
The analysis is carried out by means of Boundary Elements, using the concepts derived from Interfacial Fracture Mechanics.
In this paper, the application of these techniques to continuous elements using the example of a cantilever beam is considered.
The rudimentary design knowledge required to position a particular set of shipboard elements using the proposed methods is ideally suited to early-stage design processes.
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The promoter regions of these genes were therefore analyzed for the presence of enriched cis-elements using the Athena [78] and POBO [79] promoter analysis programs.
For selected clusters, motif finding algorithms were used to uncover additional potential cis-elements using the MEME and RSAT tool suites [ 60, 61].
The sequence of the isolated regulatory region was analyzed to predict the core promoter and cis-elements using the PlantCARE software.
Promoter regions (−1,000 to +200) of the RGL2-regulated genes, were used for ab initio detection of putative cis-elements using the Dragon Motif Builder algorithms.
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