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Regions of transcription factor binding were identified with the MACS peak caller.
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No binding was identified with the P SR2 promoter, whereas DNA retardation occurred when the P SEx1 promoter was used in the assay (Figure 7b).
Two genes associated with "response to hypoxia" and two genes associated with "oxygen binding" were identified from our candidate gene list (Table 2).
In addition, several compounds interfering with NS1/viral RNA binding were identified either through virtual or high-throughput screening methods 113, 114.
Twofold MHC class II binding peptides were identified with the rule using our method, compared to the existing scoring matrix method.
Sites matching the putative C57Bl/6 PRDM9 binding site were identified with MAST, using standard parameters.
Predicted transcription factor binding sites were identified with AliBaba2 software (http://www.gene-regulation.com/pub/programs/alibaba2/index.html) with a homology of 75%.
Ribosomal binding sites were identified with RBSfinder [ 88] and tRNA genes were searched for using tRNAscan-SE [ 89].
10,634 genomic LRH-1 binding sites were identified with a high degree of confidence (p-value ≤ 1 × 10-10, FDR ≤ 1%) (Table 1 and Figure 1).
In contrast to these results, no chaperones or protein binding genes were identified with elevated dN/dS along the clade C lineage.
ATF4 binding motifs were identified with HOMER version 4.7 using the program findMotifsGenome.pl with the following options: -size 50 -mask Data were visualized with the Integrative Genomics Viewer (IGV) version 2.3.47 (Robinson et al., 2011).
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