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These results further confirmed the efficacy of the modified search model.
In total, 1696 bidirectional transcript pairs were identified using a modified search model.
In total, 1696 bidirectional transcript pairs (BDTPs) were identified using a modified search model.
Using the modified search model, we identified 1696 BDTPs from 63541 maize transcripts (Table 2; Additional file 1).
Our comparative study of five plant genomes confirmed that the modified search model generated more comprehensive data sets (Tables 1 and 2).
Comparison of the sets of BDGs identified by the Trinklein search model with those identified using our modified search model showed that the former were subsets of the latter and that the modified search model identified 81, 30, 7, and 46 additional BDGs in sorghum, rice, soybean, and Arabidopsis, respectively (Table 2).
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To address this, Paul et al. put forward a modified search-and-capture model with explicit correction mechanisms [ 18].
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The structure of Fz4CRD was determined by molecular replacement (MR) in PHASER (McCoy, 2007) using mouse Fz8CRD (PDB ID: 1IJY) as the search model, which was modified by CHAINSAW.
A structural model of human Rac1 from X-ray crystallography [Protein Data Bank (PDB) entry 3TH5], modified to exclude bound nucleotide and magnesium, served as a molecular replacement search model using PHENIX AutoMR.
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