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Calculations of the fractional percentage of secondary structures were performed using the computer programs Spectra-Manager (Jasco) and K2d2 [65].
To identify potential binding sites for various UPR-inducible transcription factors, we analyzed the human, mouse and rat VEGFA promoters using the computer programs rVista and TRANSFAC (Figure S4).
We have screened for intra-CNE human-Fugu conserved putative TFBSs using the computer programs Consite and rVista v 2. In order to increase the sensitivity and to reduce the number of false positives, we have combined the TFBSs motif searches with phylogenetic footprinting of CNEs across distantly related species [46], [47].
Statistical analysis was conducted using the computer programs SPSS 20.0 and Lisrel 8.7.
Hormonal concentrations were analyzed by Duncan test using the computer programs SigmaStat and SigmaPlot 9.0.
Forward and reverse sequences have been assembled using the computer programs Sequence Navigator (Applied Biosystems, USA) and Sequencher (GenCodes, USA).
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The moment curvature analyses for columns and beams are conducted using the computer program Response.
Comparison has been made with accurate three-dimensional numerical modeling of the arch using the computer program ANSYS.
The essential parameters for the peaks were defined using the computer program PeakFit (Systat Software Inc).
The energy levels are calculated using the computer program PHINT [25].
The numerical values given have been calculated using the computer program MAPLE 13.
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